single nucleotide polymorphism

Summary

Summary: A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population.

Top Publications

  1. ncbi Complement factor H variant increases the risk of age-related macular degeneration
    Jonathan L Haines
    Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, TN 37232, USA
    Science 308:419-21. 2005
  2. pmc Prioritizing GWAS results: A review of statistical methods and recommendations for their application
    Rita M Cantor
    Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
    Am J Hum Genet 86:6-22. 2010
  3. pmc PLINK: a tool set for whole-genome association and population-based linkage analyses
    Shaun Purcell
    Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA
    Am J Hum Genet 81:559-75. 2007
  4. ncbi Principal components analysis corrects for stratification in genome-wide association studies
    Alkes L Price
    Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nat Genet 38:904-9. 2006
  5. pmc dbSNP: the NCBI database of genetic variation
    S T Sherry
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
    Nucleic Acids Res 29:308-11. 2001
  6. pmc Potential etiologic and functional implications of genome-wide association loci for human diseases and traits
    Lucia A Hindorff
    Office of Population Genomics, Genome Technology Branch, National Human Genome Research Institute, and National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20892, USA
    Proc Natl Acad Sci U S A 106:9362-7. 2009
  7. pmc SNAP: a web-based tool for identification and annotation of proxy SNPs using HapMap
    Andrew D Johnson
    The Framingham Heart Study of the National Heart, Lung, and Blood Institute of the National Institutes of Health, USA
    Bioinformatics 24:2938-9. 2008
  8. ncbi GenABEL: an R library for genome-wide association analysis
    Yurii S Aulchenko
    Department of Epidemiology and Biostatistics, Erasmus MC Rotterdam, Postbus 2040, 3000 CA Rotterdam, The Netherlands
    Bioinformatics 23:1294-6. 2007
  9. pmc PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data
    Kai Wang
    Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
    Genome Res 17:1665-74. 2007
  10. ncbi Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing
    J Cristobal Vera
    Department of Biology, 208 Mueller Laboratory, Pennsylvania State University, University Park, PA 16802, USA
    Mol Ecol 17:1636-47. 2008

Detail Information

Publications329 found, 100 shown here

  1. ncbi Complement factor H variant increases the risk of age-related macular degeneration
    Jonathan L Haines
    Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, TN 37232, USA
    Science 308:419-21. 2005
    ..45 and 5.57. This common variant likely explains approximately 43% of AMD in older adults...
  2. pmc Prioritizing GWAS results: A review of statistical methods and recommendations for their application
    Rita M Cantor
    Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
    Am J Hum Genet 86:6-22. 2010
    ..Reviews of published methods with recommendations for their application are provided within the framework for each approach...
  3. pmc PLINK: a tool set for whole-genome association and population-based linkage analyses
    Shaun Purcell
    Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA
    Am J Hum Genet 81:559-75. 2007
    ..Analysis of the patterns of segmental sharing has the potential to map disease loci that contain multiple rare variants in a population-based linkage analysis...
  4. ncbi Principal components analysis corrects for stratification in genome-wide association studies
    Alkes L Price
    Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nat Genet 38:904-9. 2006
    ..Our simple, efficient approach can easily be applied to disease studies with hundreds of thousands of markers...
  5. pmc dbSNP: the NCBI database of genetic variation
    S T Sherry
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
    Nucleic Acids Res 29:308-11. 2001
    ..The complete contents of dbSNP are available to the public at website: http://www.ncbi.nlm.nih.gov/SNP. The complete contents of dbSNP can also be downloaded in multiple formats via anonymous FTP at ftp://ncbi.nlm.nih.gov/snp/...
  6. pmc Potential etiologic and functional implications of genome-wide association loci for human diseases and traits
    Lucia A Hindorff
    Office of Population Genomics, Genome Technology Branch, National Human Genome Research Institute, and National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20892, USA
    Proc Natl Acad Sci U S A 106:9362-7. 2009
    ..This new online resource, together with bioinformatic predictions of the underlying functionality at trait/disease-associated loci, is well-suited to guide future investigations of the role of common variants in complex disease etiology...
  7. pmc SNAP: a web-based tool for identification and annotation of proxy SNPs using HapMap
    Andrew D Johnson
    The Framingham Heart Study of the National Heart, Lung, and Blood Institute of the National Institutes of Health, USA
    Bioinformatics 24:2938-9. 2008
    ....
  8. ncbi GenABEL: an R library for genome-wide association analysis
    Yurii S Aulchenko
    Department of Epidemiology and Biostatistics, Erasmus MC Rotterdam, Postbus 2040, 3000 CA Rotterdam, The Netherlands
    Bioinformatics 23:1294-6. 2007
    ..We evaluated GenABEL using one simulated and two real data sets. We conclude that GenABEL enables the analysis of GWA data on desktop computers...
  9. pmc PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data
    Kai Wang
    Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
    Genome Res 17:1665-74. 2007
    ..3%. Our results demonstrate the feasibility of whole-genome fine-mapping of CNVs via high-density SNP genotyping...
  10. ncbi Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing
    J Cristobal Vera
    Department of Biology, 208 Mueller Laboratory, Pennsylvania State University, University Park, PA 16802, USA
    Mol Ecol 17:1636-47. 2008
    ..This development narrows the gap between approaches based on model organisms with rich genetic resources vs. species that are most tractable for ecological and evolutionary studies...
  11. ncbi PowerMarker: an integrated analysis environment for genetic marker analysis
    Kejun Liu
    Bioinformatics Research Center, North Carolina State University Raleigh, 27695 7566, USA
    Bioinformatics 21:2128-9. 2005
    ..It accelerates the analysis lifecycle and enables users to maintain data integrity throughout the process. An ever-growing list of more than 50 different statistical analyses for genetic markers has been implemented in PowerMarker...
  12. pmc Development and characterization of a high density SNP genotyping assay for cattle
    Lakshmi K Matukumalli
    Department of Bioinformatics and Computational Biology, George Mason University, Manassas, Virginia, United States of America
    PLoS ONE 4:e5350. 2009
    ..affecting complex traits in human has spurred interest in the use of large-scale high-density single nucleotide polymorphism (SNP) genotyping for the identification of quantitative trait loci (QTL) and for marker-assisted ..
  13. ncbi Detecting recent positive selection in the human genome from haplotype structure
    Pardis C Sabeti
    Whitehead Institute MIT Center for Genome Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 419:832-7. 2002
    ..More generally, the method could be used to scan the entire genome for evidence of recent positive selection...
  14. ncbi A "silent" polymorphism in the MDR1 gene changes substrate specificity
    Chava Kimchi-Sarfaty
    Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
    Science 315:525-8. 2007
    ....
  15. pmc A common variant in the FTO gene is associated with body mass index and predisposes to childhood and adult obesity
    Timothy M Frayling
    Genetics of Complex Traits, Institute of Biomedical and Clinical Science, Peninsula Medical School, Magdalen Road, Exeter, UK
    Science 316:889-94. 2007
    ..67-fold increased odds of obesity when compared with those not inheriting a risk allele. This association was observed from age 7 years upward and reflects a specific increase in fat mass...
  16. pmc Accurate whole human genome sequencing using reversible terminator chemistry
    David R Bentley
    Illumina Cambridge Ltd Formerly Solexa Ltd, Chesterford Research Park, Little Chesterford, Nr Saffron Walden, Essex CB10 1XL, UK
    Nature 456:53-9. 2008
    ..Our approach is effective for accurate, rapid and economical whole-genome re-sequencing and many other biomedical applications...
  17. pmc Human non-synonymous SNPs: server and survey
    Vasily Ramensky
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 30:3894-900. 2002
    ..The strongest selective pressure was detected for proteins involved in transcription regulation...
  18. pmc High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome
    Evandro Novaes
    School of Forest Resources and Conservation, University of Florida, PO Box 110410, Gainesville, USA
    BMC Genomics 9:312. 2008
    ..However, it is questionable how effective the sequencing of large numbers of short reads for species with essentially no prior gene sequence information will support contig assemblies and sequence annotation...
  19. pmc Genome-wide association analysis of metabolic traits in a birth cohort from a founder population
    Chiara Sabatti
    Department of Human Genetics and Los Angeles, Los Angeles, California 90095, USA
    Nat Genet 41:35-46. 2009
    ..The association observed between low-density lipoprotein and an infrequent variant in AR suggests the potential of such a cohort for identifying associations with both common, low-impact and rarer, high-impact quantitative trait loci...
  20. ncbi The structure of haplotype blocks in the human genome
    Stacey B Gabriel
    Whitehead MIT Center for Genome Research, Cambridge, MA 02139, USA
    Science 296:2225-9. 2002
    ..Our results provide a foundation for the construction of a haplotype map of the human genome, facilitating comprehensive genetic association studies of human disease...
  21. pmc Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing
    Andreas Gnirke
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nat Biotechnol 27:182-9. 2009
    ..One lane of Illumina sequence was sufficient to call high-confidence genotypes for 89% of the targeted exon space...
  22. pmc Common regulatory variation impacts gene expression in a cell type-dependent manner
    Antigone S Dimas
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, CB10 1HH, Cambridge, UK
    Science 325:1246-50. 2009
    ..These data suggest that the complete regulatory variant repertoire can only be uncovered in the context of cell-type specificity...
  23. ncbi A new multipoint method for genome-wide association studies by imputation of genotypes
    Jonathan Marchini
    Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
    Nat Genet 39:906-13. 2007
    ..A notable future use of our method will be to boost power by combining data from genome-wide scans that use different SNP sets...
  24. pmc Genes mirror geography within Europe
    John Novembre
    Department of Ecology and Evolutionary Biology, Interdepartmental Program in Bioinformatics, University of California Los Angeles, Los Angeles, California 90095, USA
    Nature 456:98-101. 2008
    ..In addition, the results are relevant to the prospects of genetic ancestry testing; an individual's DNA can be used to infer their geographic origin with surprising accuracy-often to within a few hundred kilometres...
  25. pmc Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans
    Sekar Kathiresan
    Cardiology Division, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
    Nat Genet 40:189-97. 2008
    ..Understanding the molecular, cellular and clinical consequences of the newly identified loci may inform therapy and clinical care...
  26. pmc Mapping the genetic architecture of gene expression in human liver
    Eric E Schadt
    Rosetta Inpharmatics, Seattle, Washington, United States of America
    PLoS Biol 6:e107. 2008
    ..We also identify SORT1 and CELSR2 as candidate susceptibility genes for a locus recently associated with coronary artery disease and plasma low-density lipoprotein cholesterol levels in the process...
  27. ncbi The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)
    G A Tuskan
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    Science 313:1596-604. 2006
    ..Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport...
  28. pmc Mapping short DNA sequencing reads and calling variants using mapping quality scores
    Heng Li
    The Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
    Genome Res 18:1851-8. 2008
    ..Both read mapping and genotype calling are evaluated on simulated data and real data. MAQ is accurate, efficient, versatile, and user-friendly. It is freely available at http://maq.sourceforge.net...
  29. pmc Population analysis of large copy number variants and hotspots of human genetic disease
    Andy Itsara
    Department of Genome Sciences, School of Medicine, University of Washington, Seattle, WA 98195, USA
    Am J Hum Genet 84:148-61. 2009
    ..g., 3q29, 16p12, and 15q25.2) for further investigation. This study provides one of the first analyses of large, rare (0.1%-1%) CNVs in the general population, with insights relevant to future analyses of genetic disease...
  30. pmc Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci
    John B Harley
    Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, Oklahoma 73104, USA
    Nat Genet 40:204-10. 2008
    ..Our results show that numerous genes, some with known immune-related functions, predispose to SLE...
  31. pmc Efficient control of population structure in model organism association mapping
    Hyun Min Kang
    Department of Computer Science, University of California, Los Angeles, California 90095 1596, USA
    Genetics 178:1709-23. 2008
    ..An R package implementation and webserver of our EMMA method are publicly available...
  32. pmc Rare variants of IFIH1, a gene implicated in antiviral responses, protect against type 1 diabetes
    Sergey Nejentsev
    Juvenile Diabetes Research Foundation Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
    Science 324:387-9. 2009
    ..This finding firmly establishes the role of IFIH1 in T1D and demonstrates that resequencing studies can pinpoint disease-causing genes in genomic regions initially identified by GWASs...
  33. ncbi A mutation creating a potential illegitimate microRNA target site in the myostatin gene affects muscularity in sheep
    Alex Clop
    Unit of Animal Genomics, Department of Animal Production, Faculty of Veterinary Medicine and Centre for Biomedical Integrative Genoproteomics, University of Li├Ęge B43, 20 Boulevard de Colonster, 4000 Liege, Belgium
    Nat Genet 38:813-8. 2006
    ..Analysis of SNP databases for humans and mice demonstrates that mutations creating or destroying putative miRNA target sites are abundant and might be important effectors of phenotypic variation...
  34. pmc High-resolution mapping of expression-QTLs yields insight into human gene regulation
    Jean Baptiste Veyrieras
    Department of Human Genetics, The University of Chicago, Chicago, IL, USA
    PLoS Genet 4:e1000214. 2008
    ..Our results suggest an important role for mRNA stability in determining steady-state mRNA levels, and highlight the potential of eQTL mapping as a high-resolution tool for studying the determinants of gene regulation...
  35. pmc A simple correction for multiple testing for single-nucleotide polymorphisms in linkage disequilibrium with each other
    Dale R Nyholt
    Genetic Epidemiology Laboratory, Queensland Institute of Medical Research, Brisbane, Queensland, Australia
    Am J Hum Genet 74:765-9. 2004
    ..Additionally, output from SNPSpD includes eigenvalues, principal-component coefficients, and factor "loadings" after varimax rotation, enabling the selection of a subset of SNPs that optimize the information in a genomic region...
  36. pmc Complement factor H polymorphism in age-related macular degeneration
    Robert J Klein
    Laboratory of Statistical Genetics, Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    Science 308:385-9. 2005
    ..This polymorphism is in a region of CFH that binds heparin and C-reactive protein. The CFH gene is located on chromosome 1 in a region repeatedly linked to AMD in family-based studies...
  37. pmc A map of recent positive selection in the human genome
    Benjamin F Voight
    Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
    PLoS Biol 4:e72. 2006
    ..We describe a new analytical method for scanning single nucleotide polymorphism (SNP) data for signals of recent selection, and apply this to data from the International HapMap ..
  38. pmc The genetic structure and history of Africans and African Americans
    Sarah A Tishkoff
    Department of Biology, University of Maryland, College Park, MD 20742, USA
    Science 324:1035-44. 2009
    ..This study helps tease apart the complex evolutionary history of Africans and African Americans, aiding both anthropological and genetic epidemiologic studies...
  39. ncbi A large-scale genome-wide association study of Asian populations uncovers genetic factors influencing eight quantitative traits
    Yoon Shin Cho
    Center for Genome Science, National Institute of Health, Seoul, Korea
    Nat Genet 41:527-34. 2009
    ..2 x 10(-3), P = 1.4 x 10(-7) and P = 6.0 x 10(-4), respectively). This large-scale GWA analysis of well-characterized Korean population-based samples highlights previously unknown biological pathways...
  40. pmc Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts
    Yurii S Aulchenko
    1 Department of Epidemiology and Biostatistics, Erasmus University Medical Center, P O Box 2040, 3000 CA Rotterdam, The Netherlands 2 These authors contributed equally to this work
    Nat Genet 41:47-55. 2009
    ..001) and coronary heart disease incidence (P = 0.04). The genetic risk score improves the screening of high-risk groups of dyslipidemia over classical risk factors...
  41. ncbi Genetic variants regulating ORMDL3 expression contribute to the risk of childhood asthma
    Miriam F Moffatt
    National Heart and Lung Institute, Imperial College, London SW3 6LY, UK
    Nature 448:470-3. 2007
    ..The results indicate that genetic variants regulating ORMDL3 expression are determinants of susceptibility to childhood asthma...
  42. ncbi Multifactor dimensionality reduction software for detecting gene-gene and gene-environment interactions
    Lance W Hahn
    Program in Human Genetics and Department of Molecular Physiology and Biophysics, Vanderbilt University Medical School, Nashville, TN 37232 0700, USA
    Bioinformatics 19:376-82. 2003
    ..In this paper, we describe the MDR approach and an MDR software package...
  43. pmc Gene ontology analysis of GWA study data sets provides insights into the biology of bipolar disorder
    Peter Holmans
    MRC Centre for Neuropsychiatric Genetics and Genomics, Department of Psychological Medicine and Neurology, School of Medicine, Heath Park, CF23 6BQ Cardiff, UK
    Am J Hum Genet 85:13-24. 2009
    ..The method was also applied to a meta-analysis of bipolar disorder, and it implicated the modulation of transcription and cellular activity, including that which occurs via hormonal action, as an important player in pathogenesis...
  44. pmc Rare variants create synthetic genome-wide associations
    Samuel P Dickson
    Institute for Genome Sciences and Policy, Center for Human Genome Variation, Duke University, Durham, North Carolina, USA
    PLoS Biol 8:e1000294. 2010
    ..In conclusion, uncommon or rare genetic variants can easily create synthetic associations that are credited to common variants, and this possibility requires careful consideration in the interpretation and follow up of GWAS signals...
  45. ncbi High-resolution genotyping by amplicon melting analysis using LCGreen
    Carl T Wittwer
    Department of Pathology, University of Utah Medical School, Salt Lake City, UT 84132, USA
    Clin Chem 49:853-60. 2003
    ..Our aim was to develop a closed-tube system for genotyping and mutation scanning that did not require labeled oligonucleotides...
  46. pmc Six new loci associated with body mass index highlight a neuronal influence on body weight regulation
    Cristen J Willer
    Genetic Investigation of ANthropometric Traits Consortium
    Nat Genet 41:25-34. 2009
    ..Several of the likely causal genes are highly expressed or known to act in the central nervous system (CNS), emphasizing, as in rare monogenic forms of obesity, the role of the CNS in predisposition to obesity...
  47. pmc A multistage genome-wide association study in breast cancer identifies two new risk alleles at 1p11.2 and 14q24.1 (RAD51L1)
    Gilles Thomas
    Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, USA
    Nat Genet 41:579-84. 2009
    ..1 (rs999737; P = 1.74 x 10(-7)) localizes to RAD51L1, a gene in the homologous recombination DNA repair pathway. We also confirmed associations with loci on chromosomes 2q35, 5p12, 5q11.2, 8q24, 10q26 and 16q12.1...
  48. ncbi Worldwide human relationships inferred from genome-wide patterns of variation
    Jun Z Li
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 5120, USA
    Science 319:1100-4. 2008
    ..This data set allows the most comprehensive characterization to date of human genetic variation...
  49. pmc Genome-wide association scan of tag SNPs identifies a susceptibility locus for lung cancer at 15q25.1
    Christopher I Amos
    Department of Epidemiology, The University of Texas M D Anderson Cancer Center, Houston, Texas 77030, USA
    Nat Genet 40:616-22. 2008
    ..Haplotype analysis was consistent with there being a single risk variant in this region. We conclude that variation in a region of 15q25.1 containing nicotinic acetylcholine receptors genes contributes to lung cancer risk...
  50. pmc FASTSNP: an always up-to-date and extendable service for SNP function analysis and prioritization
    Hsiang Yu Yuan
    Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
    Nucleic Acids Res 34:W635-41. 2006
    b>Single nucleotide polymorphism (SNP) prioritization based on the phenotypic risk is essential for association studies. Assessment of the risk requires access to a variety of heterogeneous biological databases and analytical tools...
  51. ncbi A variant associated with nicotine dependence, lung cancer and peripheral arterial disease
    Thorgeir E Thorgeirsson
    deCODE Genetics, 101 Reykjavik, Iceland
    Nature 452:638-42. 2008
    ..The findings provide a case study of a gene-environment interaction, highlighting the role of nicotine addiction in the pathology of other serious diseases...
  52. pmc Core signaling pathways in human pancreatic cancers revealed by global genomic analyses
    Sian Jones
    Sol Goldman Pancreatic Cancer Research Center, Ludwig Center and Howard Hughes Medical Institute at the Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21231, USA
    Science 321:1801-6. 2008
    ..Dysregulation of these core pathways and processes through mutation can explain the major features of pancreatic tumorigenesis...
  53. ncbi Variants in KCNQ1 are associated with susceptibility to type 2 diabetes mellitus
    Kazuki Yasuda
    Department of Metabolic Disorder, Research Institute, International Medical Center of Japan, Tokyo 162 8655, Japan
    Nat Genet 40:1092-7. 2008
    ..Our data thus implicate KCNQ1 as a diabetes susceptibility gene in groups of different ancestries...
  54. pmc A flexible and accurate genotype imputation method for the next generation of genome-wide association studies
    Bryan N Howie
    Department of Statistics, University of Oxford, Oxford, UK
    PLoS Genet 5:e1000529. 2009
    ....
  55. ncbi SNPStats: a web tool for the analysis of association studies
    Xavier Sole
    Catalan Institute of Oncology, IDIBELL, Epidemiology and Cancer Registry L Hospitalet, Barcelona, Spain
    Bioinformatics 22:1928-9. 2006
    ..Analysis of multiple SNPs: haplotype frequency estimation, analysis of association of haplotypes with the response, including analysis of interactions...
  56. ncbi A single nucleotide polymorphism in the MDM2 promoter attenuates the p53 tumor suppressor pathway and accelerates tumor formation in humans
    Gareth L Bond
    Cancer Institute of New Jersey, University of Medicine and Dentistry of New Jersey, New Brunswick, NJ 08903, USA
    Cell 119:591-602. 2004
    ..In this report, a single nucleotide polymorphism (SNP309) is found in the MDM2 promoter and is shown to increase the affinity of the transcriptional ..
  57. ncbi Invited review: reliability of genomic predictions for North American Holstein bulls
    P M Vanraden
    Animal Improvement Programs Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 2350, USA
    J Dairy Sci 92:16-24. 2009
    ..Reliability increased more by doubling the number of bulls genotyped than the number of markers genotyped. Genomic prediction improves reliability by tracing the inheritance of genes even with small effects...
  58. pmc Assessing the evolutionary impact of amino acid mutations in the human genome
    Adam R Boyko
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA
    PLoS Genet 4:e1000083. 2008
    ..Here, we present a method for inferring this distribution using Single Nucleotide Polymorphism (SNP) data from a population with non-stationary demographic history (such as that of modern humans)...
  59. ncbi A survey of genetic human cortical gene expression
    Amanda J Myers
    Laboratory of Neurogenetics, National Institute on Aging, Porter Neuroscience Building, National Institutes of Health Main Campus, Bethesda, Maryland 20892, USA
    Nat Genet 39:1494-9. 2007
    ....
  60. ncbi Genetics of gene expression and its effect on disease
    Valur Emilsson
    deCODE Genetics, 101 Reykjavik, Iceland
    Nature 452:423-8. 2008
    ..A core network module in humans and mice was identified that is enriched for genes involved in the inflammatory and immune response and has been found to be causally associated to obesity-related traits...
  61. ncbi SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries
    Curtis P van Tassell
    Bovine Functional Genomics Laboratory, United States Department of Agriculture, Agricultural Research Service, 10300 Baltimore Avenue, Beltsville, Maryland 20705, USA
    Nat Methods 5:247-52. 2008
    ..67. This approach for simultaneous de novo discovery of high-quality SNPs and population characterization of allele frequencies may be applied to any species with at least a partially sequenced genome...
  62. pmc Population genomics of human gene expression
    Barbara E Stranger
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nat Genet 39:1217-24. 2007
    ..We also explore several methodologies that improve the current state of analysis of gene expression variation...
  63. ncbi Human catechol-O-methyltransferase haplotypes modulate protein expression by altering mRNA secondary structure
    A G Nackley
    Center for Neurosensory Disorders, University of North Carolina, Chapel Hill, NC 27599, USA
    Science 314:1930-3. 2006
    ..These data highlight the functional significance of synonymous variations and suggest the importance of haplotypes over single-nucleotide polymorphisms for analysis of genetic variations...
  64. ncbi A susceptibility locus for lung cancer maps to nicotinic acetylcholine receptor subunit genes on 15q25
    Rayjean J Hung
    International Agency for Research on Cancer IARC, Lyon 69008, France
    Nature 452:633-7. 2008
    ..Our results provide compelling evidence of a locus at 15q25 predisposing to lung cancer, and reinforce interest in nicotinic acetylcholine receptors as potential disease candidates and chemopreventative targets...
  65. pmc Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants
    Sekar Kathiresan
    Cardiovascular Research Center and Cardiology Division, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
    Nat Genet 41:334-41. 2009
    ..SNPs at nine loci were reproducibly associated with myocardial infarction, but tests of common and rare CNVs failed to identify additional associations with myocardial infarction risk...
  66. ncbi Single nucleotide polymorphism (SNP) discovery in the polyploid Brassica napus using Solexa transcriptome sequencing
    Martin Trick
    John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
    Plant Biotechnol J 7:334-46. 2009
    ..For a specimen region of the genome analysed in detail, segregation of alleles largely, although not entirely, followed the pattern expected for genomic markers...
  67. pmc Genetic variants near TNFAIP3 on 6q23 are associated with systemic lupus erythematosus
    Robert R Graham
    Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
    Nat Genet 40:1059-61. 2008
    ..These results establish that variants near TNFAIP3 contribute to differential risk of SLE and RA...
  68. pmc Genome-wide detection and characterization of positive selection in human populations
    Pardis C Sabeti
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
    Nature 449:913-8. 2007
    ....
  69. ncbi Predicting the insurgence of human genetic diseases associated to single point protein mutations with support vector machines and evolutionary information
    E Capriotti
    Laboratory of Biocomputing, CIRB Department of Biology, University of Bologna via Irnerio 42, 40126 Bologna, Italy
    Bioinformatics 22:2729-34. 2006
    ..The quality and completeness of presently available SNPs databases allows the application of machine learning techniques to predict the insurgence of human diseases due to single point protein mutation starting from the protein sequence...
  70. ncbi SNPs in KCNQ1 are associated with susceptibility to type 2 diabetes in East Asian and European populations
    Hiroyuki Unoki
    Laboratory for Endocrinology and Metabolism, Center for Genomic Medicine, RIKEN, Yokohama, Kanagawa 230 0045, Japan
    Nat Genet 40:1098-102. 2008
    ..5 x 10(-3); OR = 1.14, rs2237897, P = 2.4 x 10(-4); OR = 1.22) and Danish populations (additive model: rs2237895, P = 3.7 x 10(-11); OR = 1.24, rs2237897, P = 1.2 x 10(-4); OR = 1.36)...
  71. ncbi Common variants on chromosome 5p12 confer susceptibility to estrogen receptor-positive breast cancer
    Simon N Stacey
    deCODE Genetics, Sturlugata 8, 101 Reykjavik, Iceland
    Nat Genet 40:703-6. 2008
    ..The nearest gene, MRPS30, was previously implicated in apoptosis, ER-positive tumors and favorable prognosis. A recently reported signal in FGFR2 was also found to associate specifically with ER-positive breast cancer...
  72. pmc A second generation human haplotype map of over 3.1 million SNPs
    Kelly A Frazer
    The Scripps Research Institute, 10550 North Torrey Pines Road MEM275, La Jolla, California 92037, USA
    Nature 449:851-61. 2007
    ..Finally, we demonstrate increased differentiation at non-synonymous, compared to synonymous, SNPs, resulting from systematic differences in the strength or efficacy of natural selection between populations...
  73. ncbi The sequence of the human genome
    J C Venter
    Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA
    Science 291:1304-51. 2001
    ..Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge...
  74. pmc A whole-genome association study of major determinants for host control of HIV-1
    Jacques Fellay
    Center for Population Genomics and Pharmacogenetics, Duke Institute for Genome Sciences and Policy, Duke University, Durham, NC 27710, USA
    Science 317:944-7. 2007
    ..These findings emphasize the importance of studying human genetic variation as a guide to combating infectious agents...
  75. pmc Genetic variation in GIPR influences the glucose and insulin responses to an oral glucose challenge
    Richa Saxena
    Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
    Nat Genet 42:142-8. 2010
    ..Of the three newly implicated loci (GIPR, ADCY5 and VPS13C), only ADCY5 was found to be associated with type 2 diabetes in collaborating studies (n = 35,869 cases, 89,798 controls, OR = 1.12, 95% CI 1.09-1.15, P = 4.8 x 10(-18))...
  76. pmc Genome-wide association scan identifies a colorectal cancer susceptibility locus on 11q23 and replicates risk loci at 8q24 and 18q21
    Albert Tenesa
    Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Edinburgh EH4 2XU, UK
    Nat Genet 40:631-7. 2008
    ..008) and rs4939827 (P < 0.009). Carrying all six possible risk alleles yielded OR = 2.6 (95% CI = 1.75-3.89) for CRC. These findings extend our understanding of the role of common genetic variation in CRC etiology...
  77. pmc Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma
    Rameen Beroukhim
    Broad Institute, Massachusetts Institute of Technology and Harvard University, 7 Cambridge Center, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 104:20007-12. 2007
    ..Our results support the feasibility and utility of systematic characterization of the cancer genome...
  78. ncbi Genome-wide association yields new sequence variants at seven loci that associate with measures of obesity
    Gudmar Thorleifsson
    deCODE Genetics, Reykjavik, Iceland
    Nat Genet 41:18-24. 2009
    ..6 x 10(-7). This includes previously identified variants close to or in the FTO, MC4R, BDNF and SH2B1 genes, in addition to variants at seven loci not previously connected with obesity...
  79. pmc Relative impact of nucleotide and copy number variation on gene expression phenotypes
    Barbara E Stranger
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Science 315:848-53. 2007
    ..Interrogation of the genome for both types of variants may be an effective way to elucidate the causes of complex phenotypes and disease in humans...
  80. pmc Global variation in copy number in the human genome
    Richard Redon
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nature 444:444-54. 2006
    ..The data obtained delineate linkage disequilibrium patterns for many CNVs, and reveal marked variation in copy number among populations. We also demonstrate the utility of this resource for genetic disease studies...
  81. ncbi The genetic architecture of maize flowering time
    Edward S Buckler
    U S Department of Agriculture USDA Agricultural Research Service USDA ARS, USA
    Science 325:714-8. 2009
    ..Thus, a simple additive model accurately predicts flowering time for maize, in contrast to the genetic architecture observed in the selfing plant species rice and Arabidopsis...
  82. pmc Shared and distinct genetic variants in type 1 diabetes and celiac disease
    Deborah J Smyth
    Juvenile Diabetes Research Foundation Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke s Hospital, Cambridge, United Kingdom
    N Engl J Med 359:2767-77. 2008
    ..Since both diseases are associated with the HLA class II genes on chromosome 6p21, we tested whether non-HLA loci are shared...
  83. pmc Targeted capture and massively parallel sequencing of 12 human exomes
    Sarah B Ng
    Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
    Nature 461:272-6. 2009
    ..This strategy may be extendable to diseases with more complex genetics through larger sample sizes and appropriate weighting of non-synonymous variants by predicted functional impact...
  84. ncbi SLC24A5, a putative cation exchanger, affects pigmentation in zebrafish and humans
    Rebecca L Lamason
    Jake Gittlen Cancer Research Foundation, Department of Pathology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
    Science 310:1782-6. 2005
    ....
  85. pmc Genomewide SNP variation reveals relationships among landraces and modern varieties of rice
    Kenneth L McNally
    International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, The Philippines
    Proc Natl Acad Sci U S A 106:12273-8. 2009
    ..These comprehensive SNP data provide a foundation for deep exploration of rice diversity and gene-trait relationships and their use for future rice improvement...
  86. ncbi Identification of loci associated with schizophrenia by genome-wide association and follow-up
    Michael C O'Donovan
    Department of Psychological Medicine, School of Medicine, Cardiff University, Cardiff, UK
    Nat Genet 40:1053-5. 2008
    ..Meta-analysis provided strongest evidence for association around ZNF804A (P = 1.61 x 10(-7)) and this strengthened when the affected phenotype included bipolar disorder (P = 9.96 x 10(-9))...
  87. pmc Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions
    Soumya Raychaudhuri
    Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
    PLoS Genet 5:e1000534. 2009
    ..An online version of this method is available for public use (http://www.broad.mit.edu/mpg/grail/)...
  88. pmc Single nucleotide polymorphism genotyping in polyploid wheat with the Illumina GoldenGate assay
    Eduard Akhunov
    Department of Plant Sciences, University of California, Davis, CA 95616, USA
    Theor Appl Genet 119:507-17. 2009
    ....
  89. pmc SNAP: predict effect of non-synonymous polymorphisms on function
    Yana Bromberg
    Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th St, New York, NY 10032, USA
    Nucleic Acids Res 35:3823-35. 2007
    ..This measure will allow users to focus on the most accurate predictions and/or the most severe effects. Available at http://www.rostlab.org/services/SNAP...
  90. pmc PANTHER: a library of protein families and subfamilies indexed by function
    Paul D Thomas
    Protein Informatics, Celera Genomics, Foster City, California 94404, USA
    Genome Res 13:2129-41. 2003
    ..Third, we use the family HMMs to rank missense single nucleotide polymorphisms (SNPs), on a database-wide scale, according to their likelihood of affecting protein function...
  91. pmc Concept, design and implementation of a cardiovascular gene-centric 50 k SNP array for large-scale genomic association studies
    Brendan J Keating
    The Institute for Translational Medicine and Therapeutics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvannia, USA
    PLoS ONE 3:e3583. 2008
    ..We have designed a gene-centric 50 K single nucleotide polymorphism (SNP) array to assess potentially relevant loci across a range of cardiovascular, metabolic and ..
  92. ncbi Genome sequence, comparative analysis and haplotype structure of the domestic dog
    Kerstin Lindblad-Toh
    Broad Institute of Harvard and MIT, 320 Charles Street, Cambridge, Massachusetts 02141, USA
    Nature 438:803-19. 2005
    ..The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health...
  93. pmc Genomic scans for selective sweeps using SNP data
    Rasmus Nielsen
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA
    Genome Res 15:1566-75. 2005
    ..Evidence for selective sweeps is also found in many other regions, including genes known to be associated with disease risk such as DPP10 and COL4A3...
  94. ncbi Predicting the effects of amino acid substitutions on protein function
    Pauline C Ng
    Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    Annu Rev Genomics Hum Genet 7:61-80. 2006
    ..We discuss the utility of AAS prediction methods for Mendelian and complex diseases as well as their broader applications for understanding protein function...
  95. ncbi A genome-wide association study identifies colorectal cancer susceptibility loci on chromosomes 10p14 and 8q23.3
    Ian P M Tomlinson
    Molecular and Population Genetics Laboratory, London Research Institute, Cancer Research UK, London WC2A 3PX, UK
    Nat Genet 40:623-30. 2008
    ..3 (P = 3.3 x 10(-18) overall; P = 9.6 x 10(-17) replication), which tags a plausible causative gene, EIF3H. These data provide further evidence for the 'common-disease common-variant' model of CRC predisposition...
  96. pmc Practical aspects of imputation-driven meta-analysis of genome-wide association studies
    Paul I W de Bakker
    Division of Genetics, Department of Medicine, Brigham and Women s Hospital, Harvard Medical School Partners Healthcare Systems Center for Genetics and Genomics, Boston, MA 02115, USA
    Hum Mol Genet 17:R122-8. 2008
    ..As many groups are forming collaborations to engage in these efforts, this review collects a series of guidelines, practical detail and learned experiences from a variety of individuals who have contributed to the subject...
  97. pmc Structural variation of chromosomes in autism spectrum disorder
    Christian R Marshall
    The Centre for Applied Genomics, The Hospital for Sick Children, Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
    Am J Hum Genet 82:477-88. 2008
    ..Structural variants were found in sufficiently high frequency influencing ASD to suggest that cytogenetic and microarray analyses be considered in routine clinical workup...
  98. ncbi Efficient mapping of mendelian traits in dogs through genome-wide association
    Elinor K Karlsson
    Broad Institute of Harvard and Massachusetts Institute of Technology MIT, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nat Genet 39:1321-8. 2007
    ....
  99. ncbi Human genetic variation and its contribution to complex traits
    Kelly A Frazer
    Scripps Genomic Medicine, Scripps Translational Science Institute and The Scripps Research Institute, La Jolla, California 92037, USA
    Nat Rev Genet 10:241-51. 2009
    ..Technological advances, such as the ability to detect rare and structural variants, and a clear understanding of the challenges in linking different types of variation with phenotype, will be essential for future progress...
  100. pmc High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence
    David L Hyten
    Soybean Genomics and Improvement Laboratory, US Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, USA
    BMC Genomics 11:38. 2010
    ..The discovery and genetic mapping of more single nucleotide polymorphism (SNP) markers were needed to anchor and orient the remaining genome sequence...
  101. pmc The pattern of polymorphism in Arabidopsis thaliana
    Magnus Nordborg
    Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA
    PLoS Biol 3:e196. 2005
    ..Despite this, our data support the utility of A. thaliana as a model for evolutionary functional genomics...

Research Grants70

  1. Development of a novel whole genome amplification method that mimics nature
    Huimin Kong; Fiscal Year: 2007
    ..time, product yield, as well as product quality in terms of amplification bias using a combination of single nucleotide polymorphism (SNP) markers and microsatellite markers...
  2. MOLECULAR EPIDEMIOLOGY OF AIDS-ASSOCIATED LYMPHOMA
    Otoniel Martinez Maza; Fiscal Year: 2004
    ....
  3. MOLECULAR CORRELATES OF METHOTREXATE IN CHILDHOOD ALL
    Larry Matherly; Fiscal Year: 2007
    ..Studies were initiated to explore the contributions of (d) the high frequency C677T single nucleotide polymorphism in the methylene tetrahydrofolate reductase (MTHFR) gene and (e) the family of multidrug resistance ..
  4. Genetic variation and regulatory networks: Mechanisms and complexity
    DANA PE ER; Fiscal Year: 2009
    ..a novel relationship between the sequence specific RNA factor PUF3 and P-Bodies, as well as a Single Nucleotide Polymorphism (SNP) in MKT1 that modulates this relationship...
  5. Genetics and Haloperidol Response
    Robert J Hitzemann; Fiscal Year: 2012
    ..The research plan contains four specific aims. 1) To use transcriptome sequencing to determine the single nucleotide polymorphism (SNP) structure within transcribed sequences (striatum) in the DBA/2J (D2), BALB/cJ and LP/J (LP) ..
  6. Triggers of Abruptio Placentae - A Case Crossover Study of an Ischemic Placental
    Michelle A Williams; Fiscal Year: 2013
    ..In Stage 1, we will use a high-density single nucleotide polymorphism (SNP) "1536-chip" on the 1st half of samples to scan maternal and infant SNPs and SNP haplotypes for ..
  7. Diverse Roles for RIC8 During G Protein Signaling in Fungi
    Katherine A Borkovich; Fiscal Year: 2012
    ..A new Single Nucleotide Polymorphism Cleaved Amplified Polymorphic Sequence-based method (SNP-CAPS) will be used to clone suppressors ..
  8. Dependency of O-3 Induced Lung Mucus Hypersecretion on NQ01
    W Michael Foster; Fiscal Year: 2010
    ..a healthy cohort of non-smoking human subjects (n=135) demonstrates that a homozygotic genotype for a single nucleotide polymorphism of the quinone oxido-reductase enzyme, NQO1, protects from the acute irritant effects on air flow that ..
  9. Molecular Pathogenesis of MDS and CMML
    Jaroslaw P Maciejewski; Fiscal Year: 2013
    ..b>Single nucleotide polymorphism arrays (SNP-A) are a new method for high resolution karyotyping and detection of unbalanced DNA ..
  10. Functional Studies of Variants of the Bipolar Risk Gene CACNA1C in Human Neurons
    JEN PAN; Fiscal Year: 2013
    ..expression, biochemical, and electrophysiological analyses, to reveal the functional role of intronic single nucleotide polymorphism (SNP) variations of CACNA1C in controlling L-type calcium channel activity in human induced neurons...
  11. Function and Structure Adaptations in Forebrain Development
    PAT R LEVITT; Fiscal Year: 2013
    ..Moreover, we discovered that a single nucleotide polymorphism (SNP rs1858830) in the 52 transcriptional regulatory region of the human MET gene is strongly ..
  12. Training/Research Center-Bone Marrow Failure Syndromes
    Jaroslaw P Maciejewski; Fiscal Year: 2013
    ..For example, we will investigate chromosomal lesions in bone marrow failure using single nucleotide polymorphism arrays (SNP-A) which as a high resolution karyotyping method allows for the detection of unbalanced ..
  13. BDNF-Estrogen Interactions with Perimenopausal Mood and Cognition
    Elizabeth M Waters; Fiscal Year: 2012
    ..A single nucleotide polymorphism, a valine (Val) to methionine (Met) substitution (Val66Met) in the BDNF gene, results in increased ..
  14. Understanding the Role of COMT Variants in Sensorimotor Gating
    XIANJIN ZHOU; Fiscal Year: 2010
    A single nucleotide polymorphism (SNP), causing a missense mutation of codon 158 Valine to Methionine in the coding region (termed val158met), exists in the human catechol-o-methyltransferase (COMT) gene...
  15. Association of a common variant of the PPAP2B gene with cardiovascular disease.
    Andrew J Morris; Fiscal Year: 2013
    ..series of genome-wide association studies (GWAS) focuses attention on a striking association between a single nucleotide polymorphism (SNP) in the PPAP2B locus and coronary artery disease...
  16. 18F-beta-Endorphin Imaging: Translational Study of an Opioid Peptide Radiotracer
    BRIAN contact REED; Fiscal Year: 2010
    ..with this radiotracer in future studies include blood-brain processes, and direct evaluation of a single nucleotide polymorphism (SNP) in MOP-r (A118G in humans, and its proposed non-human primate ortholog)...
  17. MIF in progression and treatment of ALD
    Laura E Nagy; Fiscal Year: 2013
    ....
  18. Molecular epidemiology of drug resistance and population genetic structure of Pla
    Fangli Lu; Fiscal Year: 2013
    ..vivax transmission in Yunnan and Hainan, China. 1 ..
  19. Estrogen signaling in portopulmonary hypertension
    Steven M Kawut; Fiscal Year: 2013
    ..A single nucleotide polymorphism (SNP) (rs1800440) in CYP1B1 and higher urinary 16alpha-OHE1 / 2-OHE ratio are both risk factors for ..
  20. MECHANISMS OF ARTERIAL GRAFT HEALING
    Alexander W Clowes; Fiscal Year: 2013
    ..We have studied a single nucleotide polymorphism (-838 C>A) in the promoter of the p27Kip1 gene (CDKN1B), an important cyclin-dependent kinase ..
  21. Immune and genetic determinants of murine glomerulonephritis
    Elahna Paul; Fiscal Year: 2012
    ..loci will be phenotyped with respect to GN and autoantibody production and will be genotyped using single nucleotide polymorphism (SNP) based genome-wide scans...
  22. Functional analysis of AMD-associated HTRA1 promoter polymorphism
    Noriko Esumi; Fiscal Year: 2010
    ..While several studies identified single nucleotide polymorphism (SNP) rs10490924 in the hypothetical gene LOC387715 as the AMD-associated variant on 10q26, other ..
  23. Genetic Regulation of B Lymphocyte Aortic Homing and Atheroprotection
    Coleen A McNamara; Fiscal Year: 2013
    ..In addition, we have recently identified a single nucleotide polymorphism (SNP) in the human ID3 gene that encodes an Id3 protein with attenuated function as a dimerization ..
  24. Polymorphism affecting water balance
    David M Cohen; Fiscal Year: 2013
    ....
  25. The Molecular Genetics of High Myopia
    Terri Lois Young; Fiscal Year: 2013
    ..We gained approval for a single nucleotide polymorphism (SNP) genome screen at the Center for Inherited Disease Research (CIDR) of the National Institutes of ..
  26. Genome-wide fine-mapping of metabolic traits in heterogeneous stock rats
    LEAH CATHERINE SOLBERG WOODS; Fiscal Year: 2013
    ..We plan to phenotype an additional 500 rats and genotype these 1000 animals using the Affymetrix 10K single nucleotide polymorphism array. We will identify fine-mapped loci using single and multiple locus mapping methods...
  27. Genome Transplant Dynamics: non-invasive sequencing-based diagnosis of rejection
    HANNAH AUGUSTA contact VALANTINE; Fiscal Year: 2010
    ..that maximize the sensitivity to discriminate donor and recipient DNA;(3) sensitivity of a defined single nucleotide polymorphism (SNP) panel that differentiates donor from recipient...
  28. Oxytocin Receptors and Social Behavior
    Larry J Young; Fiscal Year: 2013
    ..The first aim will determine whether a single nucleotide polymorphism in the prairie vole oxtr gene that predicts OXTR expression in the striatum (e.g...
  29. Molecular Analysis and Role of RGS6 as a Novel Growth Suppressor
    Rory A Fisher; Fiscal Year: 2013
    ..We previously described a single nucleotide polymorphism in RGS6, which leads to increased RGS6 translation, which is associated with a significant reduction ..
  30. Functional characterization of a novel gene for non-alcoholic fatty liver disease
    ALEXIS L GORDEN; Fiscal Year: 2011
    ..association study (GWAS) meta-analysis published by our group, a novel association between NAFLD and a single nucleotide polymorphism (SNP), rs2228603 was discovered...
  31. GENETIC ANALYSIS OF HIP FRAGILITY
    Tatiana M Foroud; Fiscal Year: 2010
    ..of rats in our experiments and apply modern genetics techniques like gene expression microarrays and single nucleotide polymorphism genotyping...
  32. Protective Role of Intracellular S1P in Lung Injury
    Viswanathan Natarajan; Fiscal Year: 2010
    ..SA#3 will characterize ALI associated single nucleotide polymorphism (SNPs) in SphKs and S1PL and conduct SNP-specific association studies...
  33. The Role of Genetic Variation in Alzheimer's Disease
    Robyn A Honea; Fiscal Year: 2013
    ..We will first use ADNI data to characterize the relationship between each single nucleotide polymorphism (SNP) and baseline regional brain volume, rates of hippocampal and whole brain atrophy, and change in ..
  34. Hepatocyte Growth Factor and the Pancreatic Beta Cell
    Adolfo Garcia-Ocana; Fiscal Year: 2013
    ..association study of obesity/type 2 diabetes and related quantitative traits has identified a single nucleotide polymorphism variant (Arg72Pro) in the TP53 gene in obese/Type 2 diabetic patients...
  35. Mechanisms of tissue damage leading to chronic allergic eosinophilic esophagitis
    Seema S Aceves; Fiscal Year: 2013
    ..Our third aim is based on our observation that a functional single nucleotide polymorphism (SNP) in the TGF21 promoter (C-509T) is associated with resolution of EE following swallowed topical ..
  36. Interferon Alpha as a Tool for Gene Discovery in Human Lupus
    Timothy B Niewold; Fiscal Year: 2013
    ..a local case-case design genome- wide screen of SLE patients, re-analyze available SLE genome-wide single nucleotide polymorphism (SNP) data to detect associations with serum IFNa, and use gene expression databases to select and ..
  37. Genetic Susceptibility to Mercury Toxicity in Children
    James S Woods; Fiscal Year: 2012
    ..Of particular interest is a single nucleotide polymorphism (SNP) in exon 4 of the gene encoding the heme biosynthetic pathway enzyme, coproporphyrinogen oxidase (..
  38. Lysyl Oxidase Propeptide: Breast Cancer Inhibitor
    Gail E Sonenshein; Fiscal Year: 2013
    ..A single nucleotide polymorphism (SNP) (rs1800449) G473A, resulting in an Arg158Gln substitution in a highly conserved region in the ..
  39. Moving Towards More Individualized Therapies in HIV/HCV Co-infected Patients
    Susanna Naggie; Fiscal Year: 2013
    ..A recently discovered host single nucleotide polymorphism upstream of the IL28B gene (rs12989760) has been reported as a predictor of HCV treatment response, ..
  40. The Role of EGF in Human Hepatocellular Transformation
    BRYAN CHRISTOPHER FUCHS; Fiscal Year: 2013
    ..A single nucleotide polymorphism (A to G transition at position 61) has been identified in the EGF gene...
  41. Genetics of Hypertension Risk Factors and Sequela in African Americans
    Yan Sun; Fiscal Year: 2010
    ..GWAS of heart disease in African Americans, the characteristics of the genome-wide markers, such as single nucleotide polymorphism (SNP) and copy number variation (CNV), and the performance of the necessary tools for statistical ..
  42. TNFAIP3 (A20) and Susceptibility to Systemic Lupus Erythematosus
    Patrick M Gaffney; Fiscal Year: 2012
    ..With the advent of high-density single nucleotide polymorphism (SNP) maps based on the complete sequence of the human genome and the ability to genotype these ..
  43. System Biology Approach for Signaling Transduction Study of Complex Phenotypes
    Youli Zu; Fiscal Year: 2012
    ....
  44. N-glycosylation as a downstream effector of Interleukin-7
    Haik Mkhikian; Fiscal Year: 2013
    ..the IL-7 receptor alpha (IL-7Ra) gene have been found to cause T-, B+, NK+ SCID, and more recently a single nucleotide polymorphism in the IL-7Ra gene has been associated with autoimmunity...
  45. Functional Genomics of Platelet Aggregation Using iPS and Derived Megakaryocytes
    Linzhao Cheng; Fiscal Year: 2013
    ..only marginally illuminated by genetic variants found in genome wide association studies (GWAS) using single nucleotide polymorphism (SNPs)...
  46. Defining Microbial and Host Factors in Innate Immune Responses in Lyme Arthritis
    Klemen Strle; Fiscal Year: 2013
    ..immune responses that are stimulated by the spirochetes, and that are further augmented by a single nucleotide polymorphism in the TLR1 (1805GG) gene which is present in about half of the European Caucasians...
  47. Susceptibility to methylmercury toxicity: A role for cytochrome p450 enzymes
    Matthew D Rand; Fiscal Year: 2013
    ..Our CYP single nucleotide polymorphism (SNP) probe analyses will be done as an addendum to an ongoing large-scale genotyping project with ..
  48. Genetic Epidemiology of Pelvic Organ Prolapse
    Jennifer Marie Wu; Fiscal Year: 2010
    ..A study of familial prolapse identified a single nucleotide polymorphism (SNP) in the LAMC1 gene encoding laminin, an ECM component...
  49. Genomics and Epigenomics of Fetal Growth Regulation
    Ronald M Adkins; Fiscal Year: 2010
    ..Hypotheses: 1) Variation in birth weight is associated with patterns of single nucleotide polymorphism and copy number variation. 2) Variation in birth weight is associated with patterns of DNA methylation...
  50. Targeted Therapies for Childhood Acute Lymphoblastic Leukemia
    Brent L Wood; Fiscal Year: 2010
    ..0 gene expression profiles and 500k + 100k single nucleotide polymorphism (SNP) chip analyses) to characterize approximately 200 cases of patients with higher risk ALL treated ..
  51. Nedd4-family adaptors and their regulation of T cell function.
    PAULA MARIA OLIVER; Fiscal Year: 2013
    ..Additionally, using single nucleotide polymorphism (SNP) analysis, we have identified polymorphisms within the locus that encodes Ndfip1 (located on ..
  52. Cytokine Gene Polymorphism in CRIC Cohort
    DOMINIC S RAJ; Fiscal Year: 2010
    ..For genotyping cytokine genes of interest, we will combine a candidate single nucleotide polymorphism (SNP) and tag-SNP approach, for which race-specific panels of tag-SNPs will be chosen...
  53. Design and Interpretation of SNP Association Studies of Addiction
    FRANK SCOTT SACCONE; Fiscal Year: 2013
    ..Even if a single nucleotide polymorphism (SNP) has a statistically significant association, linkage disequilibrium (LD) with other SNPs causes ..
  54. Genome Wide Association of Coronary Artery Disease and Related Risk Factors
    Ulrich Broeckel; Fiscal Year: 2012
    ..propose a family-based genome-wide high density association scan using the 1,000,000 Affymetrix SNP (single nucleotide polymorphism) chip genotyping platform in our large set of 1,000 families with MI and CAD...
  55. PacBio RS Single Molecule, Real-Time (SMRT) DNA Sequencer
    Suzanne Sandmeyer; Fiscal Year: 2012
    ....
  56. BDNF and Alcohol Addiction
    Dorit Ron; Fiscal Year: 2012
    ..2) Test whether a single nucleotide polymorphism in the BDNF gene that has been shown to impair BDNF function, and is linked to increased risk for ..
  57. Development of Population-Based Screening for DiGeorge Syndrome Type 1
    AOY MITCHELL; Fiscal Year: 2009
    ....
  58. Mechanisms Modulating the Association between the ENG Pathway and Preeclampsia
    MANDY JO SCHMELLA; Fiscal Year: 2013
    ..Second, we will conduct focused genotyping (missense single nucleotide polymorphism assessment;sequencing) of ENG to identify common and/or rare functional variants that are involved in ..
  59. Genetic Influences Over Nicotine Withdrawal
    Mariella De Biasi; Fiscal Year: 2011
    ..by genetic factors as highlighted by the recently found correlation between nicotine dependence and single nucleotide polymorphism (SNP) in the CHRNA5-CHRNA3-CHRNB4 nAChR gene cluster...
  60. Risk Factors for the Development of Lactic Acidosis and Pancreatitis Among HAART-
    William Wester; Fiscal Year: 2011
    ..on information obtained in Aims 1 and 2;we will identify mitochondrial, drug metabolism, and other single nucleotide polymorphism (SNP) variants that may alter the expression of relevant genes involved in mitochondrial function and ..
  61. SIGNALING MECHANISMS IN NEURONAL DEGENERATION
    Neil Aronin; Fiscal Year: 2013
    ..is an inherited disease, we expected that the mutant allele will differ from wild-type by at least a single nucleotide polymorphism, thereby offering a target for gene silencing by RNAi...
  62. PTPN22 and Autoimmunity
    Nunzio Bottini; Fiscal Year: 2012
    ..We predict that our results will open new avenues for designing therapies able to thwart the effects of the genetic variation, thus effectively preventing and/or treating autoimmunity in genetically predisposed individuals. ..
  63. Risk Assessment in the Genomic Era: A Qualitative Study of Patients and Providers
    Lori Leonard; Fiscal Year: 2010
    ..a family history of early onset coronary artery disease (CAD) respond to genome wide information on single nucleotide polymorphism (SNP) variants that increase risk for common diseases, including CAD...
  64. Comprehensive Characterization and Classification of the Human Transcriptome
    THOMAS RAYMOND GINGERAS; Fiscal Year: 2011
    ..For example, the identification of millions of single nucleotide polymorphism (SNPs) and the ability to genetically alter specific transcript expression by small inhibitory (si-) ..
  65. Biomarkers of Progression to Esophageal Adenocarcinoma
    GIULIANA JULIE IZZO; Fiscal Year: 2010
    ..Clearly, such tools would be of critical importance. Our recent work in BE indicates that the CD1 single nucleotide polymorphism G/A870 promotes abnormal nuclear CD1 levels and enhances the acquisition of genomic instability, ..
  66. Pharmacogenetics of the Statin Response
    ERNST SCHAEFER; Fiscal Year: 2006
    ..We propose to isolate DNA in all subjects, carry out sequencing for single nucleotide polymorphism detection in 5 male and 5 female hyper-responders and the same number of hypo-responders (LDL C <10%..
  67. Cannabinoid Mechanisms in Human Gastrointestinal Motor and Sensory Functions
    MICHAEL L CAMILLERI; Fiscal Year: 2010
    ..Anandamide is inactivated by a fatty acid amide hydrolase (FAAH) in vivo. A single nucleotide polymorphism (SNP) in the human FAAH gene (385C to A), in homozygous form, converts a conserved proline residue in ..
  68. Pharmacogenetics and Cardiovascular Events
    Bruce Psaty; Fiscal Year: 2006
    ..With resources largely devoted to recruitment, the typical grant included only 1 single nucleotide polymorphism (SNP) per gene in each of a few candidate genes-an approach that ignores the complexity of the ..
  69. Colon Cancer Prevention Program Project Grant
    M Lance; Fiscal Year: 2009
    ..As secondary objectives, the influence of single nucleotide polymorphism variations will be analyzed in six genes for which there is evidence of genotypic effect modification ..
  70. HMG-CoA reductase alternative splicing and LDL response to statin
    Ronald M Krauss; Fiscal Year: 2010
    ..Finally, we have found that the extent of exon 13 skipping is associated with a common HMGCR single nucleotide polymorphism (SNP) in intron 13 that we have also found to be associated with the magnitude of plasma LDL-C ..