Nicholas J Schork

Summary

Affiliation: The Scripps Research Institute
Country: USA

Publications

  1. pmc Identification of EpCAM as the gene for congenital tufting enteropathy
    Mamata Sivagnanam
    Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
    Gastroenterology 135:429-37. 2008
  2. pmc Common vs. rare allele hypotheses for complex diseases
    Nicholas J Schork
    Scripps Genomic Medicine, and Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, United States
    Curr Opin Genet Dev 19:212-9. 2009
  3. pmc Age-dependent brain gene expression and copy number anomalies in autism suggest distinct pathological processes at young versus mature ages
    Maggie L Chow
    Department of Neuroscience, NIH UCSD Autism Center of Excellence, School of Medicine, University of California San Diego, La Jolla, California, United States of America
    PLoS Genet 8:e1002592. 2012
  4. pmc Preprocessing and Quality Control Strategies for Illumina DASL Assay-Based Brain Gene Expression Studies with Semi-Degraded Samples
    Maggie L Chow
    Department of Neuroscience, UC San Diego Autism Center of Excellence, School of Medicine, National Institutes of Health, University of California San Diego La Jolla, CA, USA
    Front Genet 3:11. 2012
  5. pmc Statistical properties of multivariate distance matrix regression for high-dimensional data analysis
    Matthew A Zapala
    Department of Radiology, University of California at San Diego La Jolla, CA, USA
    Front Genet 3:190. 2012
  6. pmc Clinical implications of human population differences in genome-wide rates of functional genotypes
    Ali Torkamani
    The Scripps Translational Science La Jolla, CA, USA Scripps Health La Jolla, CA, USA Department of Molecular and Experimental Medicine, The Scripps Research Institute La Jolla, CA, USA
    Front Genet 3:211. 2012
  7. pmc A Method for Inferring an Individual's Genetic Ancestry and Degree of Admixture Associated with Six Major Continental Populations
    Ondrej Libiger
    Department of Molecular and Experimental Medicine, The Scripps Research Institute and the Scripps Translational Science Institute La Jolla, CA, USA
    Front Genet 3:322. 2012
  8. pmc Common variants explain a large fraction of the variability in the liability to psoriasis in a Han Chinese population
    Xianyong Yin
    Institute of Dermatology, Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui Province 230032, China
    BMC Genomics 15:87. 2014
  9. pmc Whole genome sequencing analysis of Plasmodium vivax using whole genome capture
    A Taylor Bright
    Biomedical Sciences Program, University of California, San Diego, La Jolla, CA, USA
    BMC Genomics 13:262. 2012
  10. pmc Strategies and methods to study sex differences in cardiovascular structure and function: a guide for basic scientists
    Virginia M Miller
    Departments of Surgery, Physiology and Biomedical Engineering, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
    Biol Sex Differ 2:14. 2011

Research Grants

  1. FAMILY BLOOD PRESSURE PROGRAM
    Nicholas Schork; Fiscal Year: 2004

Collaborators

Detail Information

Publications100

  1. pmc Identification of EpCAM as the gene for congenital tufting enteropathy
    Mamata Sivagnanam
    Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of California San Diego, La Jolla, California, USA
    Gastroenterology 135:429-37. 2008
    ..The pathogenesis and genetics of this disorder are not well understood. The objective of this study was to identify the gene responsible for CTE...
  2. pmc Common vs. rare allele hypotheses for complex diseases
    Nicholas J Schork
    Scripps Genomic Medicine, and Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, United States
    Curr Opin Genet Dev 19:212-9. 2009
    ..Both hypotheses have their place in current research efforts...
  3. pmc Age-dependent brain gene expression and copy number anomalies in autism suggest distinct pathological processes at young versus mature ages
    Maggie L Chow
    Department of Neuroscience, NIH UCSD Autism Center of Excellence, School of Medicine, University of California San Diego, La Jolla, California, United States of America
    PLoS Genet 8:e1002592. 2012
    ..Our results raise the hypothesis that genetic dysregulation in the developing brain leads to abnormal regional patterning, excess prefrontal neurons, cortical overgrowth, and neural dysfunction in autism...
  4. pmc Preprocessing and Quality Control Strategies for Illumina DASL Assay-Based Brain Gene Expression Studies with Semi-Degraded Samples
    Maggie L Chow
    Department of Neuroscience, UC San Diego Autism Center of Excellence, School of Medicine, National Institutes of Health, University of California San Diego La Jolla, CA, USA
    Front Genet 3:11. 2012
    ....
  5. pmc Statistical properties of multivariate distance matrix regression for high-dimensional data analysis
    Matthew A Zapala
    Department of Radiology, University of California at San Diego La Jolla, CA, USA
    Front Genet 3:190. 2012
    ..We also describe the utility of MDMR analysis in assessing hypotheses about the appropriate number of clusters arising from a cluster analysis...
  6. pmc Clinical implications of human population differences in genome-wide rates of functional genotypes
    Ali Torkamani
    The Scripps Translational Science La Jolla, CA, USA Scripps Health La Jolla, CA, USA Department of Molecular and Experimental Medicine, The Scripps Research Institute La Jolla, CA, USA
    Front Genet 3:211. 2012
    ..Our results have important implications for clinical sequencing initiatives...
  7. pmc A Method for Inferring an Individual's Genetic Ancestry and Degree of Admixture Associated with Six Major Continental Populations
    Ondrej Libiger
    Department of Molecular and Experimental Medicine, The Scripps Research Institute and the Scripps Translational Science Institute La Jolla, CA, USA
    Front Genet 3:322. 2012
    ....
  8. pmc Common variants explain a large fraction of the variability in the liability to psoriasis in a Han Chinese population
    Xianyong Yin
    Institute of Dermatology, Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui Province 230032, China
    BMC Genomics 15:87. 2014
    ..01) in a Han Chinese population...
  9. pmc Whole genome sequencing analysis of Plasmodium vivax using whole genome capture
    A Taylor Bright
    Biomedical Sciences Program, University of California, San Diego, La Jolla, CA, USA
    BMC Genomics 13:262. 2012
    ..These features have precluded the analysis of archived blood samples and require the presence of laboratories in close proximity to the collection of field samples for optimal pre-cryopreservation sample preparation...
  10. pmc Strategies and methods to study sex differences in cardiovascular structure and function: a guide for basic scientists
    Virginia M Miller
    Departments of Surgery, Physiology and Biomedical Engineering, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
    Biol Sex Differ 2:14. 2011
    ..abstract:..
  11. pmc Association of genetic variants on 15q12 with cortical thickness and cognition in schizophrenia
    Trygve E Bakken
    The Scripps Research Institute, Scripps Translational Science Institute, 3344 N Torrey Pines Court, La Jolla, CA 92037, USA
    Arch Gen Psychiatry 68:781-90. 2011
    ..Identifying genes that contribute to variation in cortical thickness provides a means to elucidate some of the biological mechanisms underlying these diseases and general cognitive abilities...
  12. pmc Gene expression profiling of human whole blood samples with the Illumina WG-DASL assay
    Mary E Winn
    Scripps Genomic Medicine and Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, CA 92037, USA
    BMC Genomics 12:412. 2011
    ..We assessed the utility of the whole genome DASL assay in an analysis of peripheral whole blood gene expression profiles...
  13. pmc Genotype-based risk and pharmacogenetic sampling in clinical trials
    Nicholas J Schork
    Scripps Translational Science Institute and Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, USA
    J Biopharm Stat 20:315-33. 2010
    ..In addition, we also derive realistic bounds for samples sizes for clinical trials investigating pharmacogenetic effects that leverage genetic variations identified in recent association studies...
  14. pmc Natural variation within the neuronal nicotinic acetylcholine receptor cluster on human chromosome 15q24: influence on heritable autonomic traits in twin pairs
    Brinda K Rana
    Departments of Psychiatry, University of California at San Diego, La Jolla, California 92093 0657, USA
    J Pharmacol Exp Ther 331:419-28. 2009
    ..These cellular events suggest a homeostatic mechanism underlying the pleiotropic actions of CHRNA3 genetic variation on autonomic function observed in twins...
  15. pmc Chromogranin A polymorphisms are associated with hypertensive renal disease
    Rany M Salem
    Department of Medicine and Center for Molecular Genetics, University of California at San Diego and Veterans Administration San Diego Healthcare System 0838, 9500 Gilman Drive, La Jolla, CA 92093 0838, USA
    J Am Soc Nephrol 19:600-14. 2008
    ..In summary, common variants in chromogranin A associate with the risk of hypertensive ESRD in blacks...
  16. pmc G-protein-coupled receptor kinase 4 polymorphisms and blood pressure response to metoprolol among African Americans: sex-specificity and interactions
    Vibha Bhatnagar
    Deparment of Family and Preventive Medicine, University of California San Diego, La Jolla, California, USA
    Am J Hypertens 22:332-8. 2009
    ..This study explores the association between G-protein-coupled receptor kinase type 4 (GRK4) variants and blood pressure response to metoprolol among African Americans with early hypertensive nephrosclerosis...
  17. pmc Adrenergic polymorphism and the human stress response
    Fangwen Rao
    Department of Medicine, University of California at San Diego, La Jolla, California 92093 0838, USA
    Ann N Y Acad Sci 1148:282-96. 2008
    ..The results suggest novel pathophysiological links between a key adrenergic locus, catecholamine metabolism, and blood pressure, and suggest new strategies to approach the mechanism, diagnosis, and treatment of systemic hypertension...
  18. pmc Genome-wide linkage analyses of 12 endophenotypes for schizophrenia from the Consortium on the Genetics of Schizophrenia
    Tiffany A Greenwood
    Department of Psychiatry, University of California San Diego, La Jolla, Calif, USA
    Am J Psychiatry 170:521-32. 2013
    ..The authors previously demonstrated the heritability of these endophenotypes; in the present study, genetic linkage was evaluated...
  19. pmc Human dopamine beta-hydroxylase (DBH) regulatory polymorphism that influences enzymatic activity, autonomic function, and blood pressure
    Yuqing Chen
    Department of Medicine, University of California at San Diego, La Jolla, California 92093 0838, USA
    J Hypertens 28:76-86. 2010
    ..Here we systematically investigated DBH polymorphisms associated with enzymatic activity as well as autonomic and blood pressure (BP)/disease phenotypes in vivo...
  20. pmc Accurate detection and genotyping of SNPs utilizing population sequencing data
    Vikas Bansal
    Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, CA 92037, USA
    Genome Res 20:537-45. 2010
    ..Collectively, these results suggest that analysis of population sequencing data is a powerful approach for the accurate detection of SNPs and the assignment of genotypes to individual samples...
  21. ncbi request reprint Population-based sample reveals gene-gender interactions in blood pressure in White Americans
    Brinda K Rana
    Department of Psychiatry, University of California at San Diego, La Jolla, CA 92093, USA
    Hypertension 49:96-106. 2007
    ..Such genetic variants may define genetically and etiologically distinct subgroups of men and women with essential hypertension and may have implications for rational treatment selection...
  22. pmc A common MECP2 haplotype associates with reduced cortical surface area in humans in two independent populations
    Alexander H Joyner
    Scripps Translational Science Institute, 3344 North Torrey Pines Court, La Jolla, CA 92037, USA
    Proc Natl Acad Sci U S A 106:15483-8. 2009
    ..Secondary analysis showed that this allele was also associated with reduced surface area in specific cortical regions (cuneus, fusiform gyrus, pars triangularis) in both populations...
  23. ncbi request reprint Renal albumin excretion: twin studies identify influences of heredity, environment, and adrenergic pathway polymorphism
    Fangwen Rao
    Department of Medicine, Center for Human Genetics and Genomics, University of California at San Diego, La Jolla, CA 92093 0838, USA
    Hypertension 49:1015-31. 2007
    ..Such functional links between adrenergic activity and glomerular injury suggest novel approaches to its prediction, prevention, diagnosis, and treatment...
  24. pmc Genetic variation within adrenergic pathways determines in vivo effects of presynaptic stimulation in humans
    Maple M Fung
    Department of Medicine, Division of Nephrology Hypertension, University of California at San Diego, 9500 Gilman Dr, La Jolla, CA 92093 0838, USA
    Circulation 117:517-25. 2008
    ..Catecholamines govern stress blood pressure responses. Catecholaminergic responses may be partially genetic and contribute to the complex heritability of hypertension...
  25. ncbi request reprint Initial heritability analyses of endophenotypic measures for schizophrenia: the consortium on the genetics of schizophrenia
    Tiffany A Greenwood
    Department of Psychiatry, University of California San Diego, La Jolla, USA
    Arch Gen Psychiatry 64:1242-50. 2007
    ..Exploration of the genetic architecture of specific endophenotypes may be a powerful strategy for understanding the genetic basis of schizophrenia...
  26. pmc Genetic implication of a novel thiamine transporter in human hypertension
    Kuixing Zhang
    Department of Medicine, University of California at San Diego UCSD, La Jolla, California
    J Am Coll Cardiol 63:1542-55. 2014
    ..This study coupled 2 strategies-trait extremes and genome-wide pooling-to discover a novel blood pressure (BP) locus that encodes a previously uncharacterized thiamine transporter...
  27. ncbi request reprint Interactive effects of common beta2-adrenoceptor haplotypes and age on susceptibility to hypertension and receptor function
    Xuping Bao
    Department of Medicine, University of California, San Diego, CA, USA
    Hypertension 46:301-7. 2005
    ..05) and decreased heart rate (7%; P<0.001). Our study suggests that age is an important modifier for the effects of ADRB2 polymorphisms on ADRB2 function and the development of hypertension...
  28. pmc Genome-wide expression assay comparison across frozen and fixed postmortem brain tissue samples
    Maggie L Chow
    Department of Neuroscience, NIH UCSD Autism Center of Excellence, School of Medicine, University of California San Diego, 8110 La Jolla Shores Dr Ste 201, La Jolla, CA 92093, USA
    BMC Genomics 12:449. 2011
    ....
  29. pmc Methylenetetrahydrofolate reductase (MTHFR) polymorphism A1298C (Glu429Ala) predicts decline in renal function over time in the African-American Study of Kidney Disease and Hypertension (AASK) Trial and Veterans Affairs Hypertension Cohort (VAHC)
    Maple M Fung
    Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
    Nephrol Dial Transplant 27:197-205. 2012
    ..Here, we evaluated the influence of MTHFR variants on progressive loss of kidney function...
  30. pmc Adrenergic beta-1 receptor genetic variation predicts longitudinal rate of GFR decline in hypertensive nephrosclerosis
    Maple M Fung
    Department of Medicine, University of California, San Diego, and San Diego Veterans Affairs Healthcare System, La Jolla, CA, USA
    Nephrol Dial Transplant 24:3677-86. 2009
    ..End-stage renal disease (ESRD) due to hypertension is common and displays familial aggregation in African Americans, suggesting genetic risk factors, including adrenergic activity alterations which are noted in both hypertension and ESRD...
  31. pmc Statistical genetics concepts and approaches in schizophrenia and related neuropsychiatric research
    Nicholas J Schork
    Department of Psychiatry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0603, USA
    Schizophr Bull 33:95-104. 2007
    ..We also provide a discussion of the most pressing contemporary problems that demand further research if progress is to be made in the identification of genes and genetic variations that predispose to complex neuropsychiatric diseases...
  32. ncbi request reprint Rho kinase polymorphism influences blood pressure and systemic vascular resistance in human twins: role of heredity
    Tammy M Seasholtz
    Department of Pharmacology, University of California, San Diego, CA, USA
    Hypertension 47:937-47. 2006
    ....
  33. pmc Evidence for association of bipolar disorder to haplotypes in the 22q12.3 region near the genes stargazin, IFT27 and parvalbumin
    Stephanie Nissen
    Department of Psychiatry, University of California San Diego, La Jolla 92093, California
    Am J Med Genet B Neuropsychiatr Genet 159:941-50. 2012
    ..The replication of association to overlapping haplotypes in three independent datasets suggests the presence of a bipolar disorder susceptibility gene in this region...
  34. pmc Neuropeptide Y (NPY): genetic variation in the human promoter alters glucocorticoid signaling, yielding increased NPY secretion and stress responses
    Kuixing Zhang
    Department of Medicine and Institute for Genomic Medicine, University of California at San Diego, San Diego, California, USA
    J Am Coll Cardiol 60:1678-89. 2012
    ..This study sought to understand whether genetic variation at the Neuropeptide Y (NPY) locus governs secretion and stress responses in vivo as well as NPY gene expression in sympathochromaffin cells...
  35. pmc Angiotensin-converting enzyme gene polymorphism predicts the time-course of blood pressure response to angiotensin converting enzyme inhibition in the AASK trial
    Vibha Bhatnagar
    University of California San Diego, La Jolla, USA
    J Hypertens 25:2082-92. 2007
    ..It has yet to be determined whether genotyping at the angiotensin-converting enzyme (ACE) locus is predictive of blood pressure response to an ACE inhibitor...
  36. pmc Analysis of 94 candidate genes and 12 endophenotypes for schizophrenia from the Consortium on the Genetics of Schizophrenia
    Tiffany A Greenwood
    Department of Psychiatry, University of California at San Diego, La Jolla, CA 92093 0804, USA
    Am J Psychiatry 168:930-46. 2011
    ....
  37. pmc A covering method for detecting genetic associations between rare variants and common phenotypes
    Gaurav Bhatia
    Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
    PLoS Comput Biol 6:e1000954. 2010
    ..The data suggests that the RVs help disrupt the expression of the two genes, leading to lowered metabolism of the corresponding cannabinoids. Overall, our results point to the power of including RVs in measuring genetic associations...
  38. pmc An ancestral variant of Secretogranin II confers regulation by PHOX2 transcription factors and association with hypertension
    Gen Wen
    Department of Medicine, Moores UCSD Cancer Center, University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093, USA
    Hum Mol Genet 16:1752-64. 2007
    ..These results identify a common regulatory variation in SCG2 and implicate granin gene expression in the control of human blood pressure and susceptibility to hypertension...
  39. ncbi request reprint COMT polymorphisms and anxiety-related personality traits
    Murray B Stein
    Department of Psychiatry, University of California, San Diego, La Jolla, CA 92093 0985, USA
    Neuropsychopharmacology 30:2092-102. 2005
    ..Other functional variants may exist that contribute to this relationship. Possible sex-specific effects remain to be further studied and explained...
  40. doi request reprint Comparison of genetic distance measures using human SNP genotype data
    Ondrej Libiger
    Scripps Translational Science Institute, Scripps Health, and Scripps Research Institute, La Jolla, CA, USA
    Hum Biol 81:389-406. 2009
    ..Finally, our study suggests that using the Cavalli-Sforza and Edwards distance may provide less power for studies concerning human migration history...
  41. pmc Suggestive evidence for association of the circadian genes PERIOD3 and ARNTL with bipolar disorder
    Caroline M Nievergelt
    Department of Psychiatry, University of California, San Diego, La Jolla, California 92093 0603, USA
    Am J Med Genet B Neuropsychiatr Genet 141:234-41. 2006
    ..However, the trends for ARNTL and PER3 are suggestive of their involvement in bipolar disorder and warrant further study in a larger sample...
  42. ncbi request reprint Comprehensive linkage and linkage heterogeneity analysis of 4344 sibling pairs affected with hypertension from the Family Blood Pressure Program
    Tiffany A Greenwood
    Polymorphism Research Laboratory, Department of Psychiatry, University of California, San Diego, La Jolla, California 92093 0603, USA
    Genet Epidemiol 31:195-210. 2007
    ..Ultimately our results suggest that evidence for linkage heterogeneity can only be detected with large sample sizes, such as the FBPP, which is consistent with theoretical sample size calculations...
  43. ncbi request reprint Genetic variation at the human alpha2B-adrenergic receptor locus: role in blood pressure variation and yohimbine response
    Jason P Etzel
    Department of Medicine, University of California at San Diego, CA, USA
    Hypertension 45:1207-13. 2005
    ..Thus, despite considerable polymorphism in alpha2-AR genes, such variation is not a major determinant of variability in yohimbine response and by inference, in susceptibility to essential hypertension...
  44. pmc Generalized genomic distance-based regression methodology for multilocus association analysis
    Jennifer Wessel
    Polymorphism Research Laboratory, Department of Psychiatry, Divisions of Epidemiology, Center for Human Genetics and Genomics, University of California at San Diego, La Jolla, CA 92093 0603, USA
    Am J Hum Genet 79:792-806. 2006
    ....
  45. pmc Longitudinal genome-wide association of cardiovascular disease risk factors in the Bogalusa heart study
    Erin N Smith
    Scripps Genomic Medicine and Scripps Translational Science Institute, La Jolla, California, United States of America
    PLoS Genet 6:e1001094. 2010
    ....
  46. pmc Coexpression network analysis of neural tissue reveals perturbations in developmental processes in schizophrenia
    Ali Torkamani
    Scripps Translational Science Institute, La Jolla, California 92037, USA
    Genome Res 20:403-12. 2010
    ..These findings provide a novel mechanism for the "developmental" hypothesis of schizophrenia on a molecular level...
  47. doi request reprint The relative importance of genetics and environment on mammographic density
    Giske Ursin
    Department of Preventive Medicine, University of Southern California Keck School of Medicine, Norris Comprehensive Cancer Center, Los Angeles, California, USA
    Cancer Epidemiol Biomarkers Prev 18:102-12. 2009
    ..We investigated whether part of the presumed heritability might be attributed to differential sharing of modifiable risk factors in monozygotic (MZ) and dizygotic (DZ) twins...
  48. pmc Patterns of population epigenomic diversity
    Robert J Schmitz
    Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
    Nature 495:193-8. 2013
    ....
  49. ncbi request reprint Biogenesis of the secretory granule: chromogranin A coiled-coil structure results in unusual physical properties and suggests a mechanism for granule core condensation
    Coleman A Mosley
    Bioinformatics Graduate Program, University of California at San Diego, La Jolla, CA 92093 0838, USA
    Biochemistry 46:10999-1012. 2007
    ..These results suggest new roles for secretory protein tertiary structure in hormone and transmitter storage, with implications for secretory cargo condensation (or dense core "packing" structure) within the regulated pathway...
  50. doi request reprint 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...
  51. pmc DNA variation and brain region-specific expression profiles exhibit different relationships between inbred mouse strains: implications for eQTL mapping studies
    Iiris Hovatta
    The Salk Institute for Biological Studies, Laboratory of Genetics, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
    Genome Biol 8:R25. 2007
    ....
  52. ncbi request reprint A simulation-based analysis of chromosome segment sharing among a group of arbitrarily related individuals
    Ondrej Libiger
    1 1Scripps Genomic Medicine, Scripps Health, La Jolla, CA, USA
    Eur J Hum Genet 15:1260-8. 2007
    ..We present results that showcase possible application of assessing genomic sharing in gene mapping and apply our analysis to data available from published gene mapping studies...
  53. ncbi request reprint Powerful designs for genetic association studies that consider twins and sibling pairs with discordant genotypes
    Jennifer Wessel
    Center for Human Genetics and Genomics, University of California San Diego, La Jolla, CA, USA
    Genet Epidemiol 31:789-96. 2007
    ....
  54. pmc Detecting genetic variation in microarray expression data
    Jennifer A Greenhall
    The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
    Genome Res 17:1228-35. 2007
    ..This approach enables the opportunistic extraction of genetic variation information from new or pre-existing gene expression data obtained with high-density oligonucleotide arrays...
  55. pmc The importance of phase information for human genomics
    Ryan Tewhey
    The Scripps Translational Science Institute, 3344 North Torrey Pines Road, Suite 300, La Jolla, California 92037, USA
    Nat Rev Genet 12:215-23. 2011
    ..Thus, the existing technological impediments to obtaining phase information must be overcome if human genomics is to reach its full potential...
  56. pmc The VA Hypertension Primary Care Longitudinal Cohort: Electronic medical records in the post-genomic era
    Rany M Salem
    University of California, San Diego, CA, USA
    Health Informatics J 16:274-86. 2010
    ..02 ± 0.12 micrograms, enough for several thousand genotypes. The coupling of detailed medical databases with genetic information has the potential to facilitate the genetic study of hypertension and other complex diseases...
  57. doi request reprint Impact of direct-to-consumer genomic testing at long term follow-up
    Cinnamon S Bloss
    Scripps Genomic Medicine, Scripps Translational Science Institute, 3344 N Torrey Pines Court, Suite 300, La Jolla, CA 92037, USA
    J Med Genet 50:393-400. 2013
    ..This study aimed to determine the long term psychological, behavioural, and clinical impacts of genomic risk testing for common disease...
  58. doi request reprint Influence of genetic polymorphisms on the effect of high- and standard-dose clopidogrel after percutaneous coronary intervention: the GIFT (Genotype Information and Functional Testing) study
    Matthew J Price
    Division of Cardiovascular Diseases, Scripps Clinic, La Jolla, California 92037, USA
    J Am Coll Cardiol 59:1928-37. 2012
    ..This study sought to evaluate the influence of single nucleotide polymorphisms (SNPs) on the pharmacodynamic effect of high- or standard-dose clopidogrel after percutaneous coronary intervention (PCI)...
  59. pmc Evaluation of next generation sequencing platforms for population targeted sequencing studies
    Olivier Harismendy
    Scripps Genomic Medicine, Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, CA 92037, USA
    Genome Biol 10:R32. 2009
    ..To evaluate these platforms for this application, we analyzed human sequence generated by the Roche 454, Illumina GA, and the ABI SOLiD technologies for the same 260 kb in four individuals...
  60. pmc Deconstructing schizophrenia: an overview of the use of endophenotypes in order to understand a complex disorder
    David L Braff
    Department of Psychiatry, University of California San Diego, 9500 Gilman Drive, Mail Code 0804, La Jolla, CA 92093, USA
    Schizophr Bull 33:21-32. 2007
    ..The endophenotype strategy offers powerful and exciting opportunities to understand the genetically conferred neurobiological vulnerabilities and possible new strong inference and molecularly based treatments for schizophrenia...
  61. pmc Pathway analysis of seven common diseases assessed by genome-wide association
    Ali Torkamani
    Scripps Genomic Medicine, The Scripps Translational Science Institute, and Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
    Genomics 92:265-72. 2008
    ..Additionally, we analyze the genetic relationships between the seven diseases, and based upon similarities with respect to the associated genes and pathways affected in each, propose a new way of categorizing the diseases...
  62. pmc Statistical analysis strategies for association studies involving rare variants
    Vikas Bansal
    The Scripps Translational Science Institute, 3344 North Torrey Pines Court, Suite 300, La Jolla, California 92037, USA
    Nat Rev Genet 11:773-85. 2010
    ..Ultimately, although a wide variety of analytical approaches exist, more work is needed to refine them and determine their properties and power in different contexts...
  63. ncbi request reprint Identification of quantitative trait Loci for anxiety and locomotion phenotypes in rat recombinant inbred strains
    Lisa H Conti
    Department of Pharmacology, 0636, University of California, San Diego, La Jolla, California, USA
    Behav Genet 34:93-103. 2004
    ..For a phenotype reflecting both anxiety and locomotion, QTL were found on chromosomes 2, 7, and 8, while for a locomotion phenotype, significant QTL were found on chromosomes 3 and 18...
  64. ncbi request reprint Accommodating pathway information in expression quantitative trait locus analysis
    Jennifer Wessel
    Polymorphism Research Laboratory, Department of Psychiatry, University of California at San Diego, La Jolla, CA 92093, USA
    Genomics 90:132-42. 2007
    ..We apply available genetic network and pathway analysis software, as well as a novel regression analysis technique, to carry out the proposed studies. We also consider extensions of the proposed strategies and areas of future research...
  65. ncbi request reprint Pleiotropic effects of novel trans-acting loci influencing human sympathochromaffin secretion
    Tiffany A Greenwood
    Department of Medicine, University of California San Diego, La Jolla, USA
    Physiol Genomics 25:470-9. 2006
    ..The results suggest a new approach to heritable autonomic control of circulation and the genetic basis of cardiovascular diseases such as systemic hypertension...
  66. pmc Noncoding transcription within the Igh distal V(H) region at PAIR elements affects the 3D structure of the Igh locus in pro-B cells
    Jiyoti Verma-Gaur
    Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
    Proc Natl Acad Sci U S A 109:17004-9. 2012
    ..Therefore, we hypothesize that one key role of noncoding germ-line transcription is to facilitate locus compaction, allowing distal V(H) genes to undergo efficient rearrangement...
  67. pmc Human haplotype block sizes are negatively correlated with recombination rates
    Tiffany A Greenwood
    Polymorphism Research Laboratory, Department of Psychiatry, University of California at San Diego, La Jolla, California 92093, USA
    Genome Res 14:1358-61. 2004
    ..We discuss the potential implications of this negative correlation in the context of the organization, properties, and potential ubiquity of a block-like structure in the human genome...
  68. pmc Accommodating linkage disequilibrium in genetic-association analyses via ridge regression
    Nathalie Malo
    Department of Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
    Am J Hum Genet 82:375-85. 2008
    ..We showcase the method by using both simulated and real data. Our results suggest that ridge regression and related techniques have the potential to distinguish causative from noncausative variations in association studies...
  69. pmc Mechanisms underlying hypoxia tolerance in Drosophila melanogaster: hairy as a metabolic switch
    Dan Zhou
    Department of Pediatrics, University of California San Diego, La Jolla, California, United States of America
    PLoS Genet 4:e1000221. 2008
    ....
  70. ncbi request reprint Gene-by-environment (serotonin transporter and childhood maltreatment) interaction for anxiety sensitivity, an intermediate phenotype for anxiety disorders
    Murray B Stein
    Anxiety and Traumatic Stress Disorders Program, Departments of Psychiatry and Family and Preventive Medicine, University of California San Diego, La Jolla, CA 92093 0855, USA
    Neuropsychopharmacology 33:312-9. 2008
    ..These findings are consistent with the notion that 5-HTTLPR operates broadly to moderate emotional responsivity to stress...
  71. pmc Simulation-based homozygosity mapping with the GAW14 COGA dataset on alcoholism
    Ondrej Libiger
    Polymorphism Research Laboratory, Department of Psychiatry, The University of California, San Diego, La Jolla, California 92093 0603, USA
    BMC Genet 6:S35. 2005
    ..Our assessment of sharing involved the use of a single-nucleotide polymorphism (SNP) marker map provided by Affymetrix...
  72. pmc Genetic structure of community acquired methicillin-resistant Staphylococcus aureus USA300
    Ryan Tewhey
    Scripps Genomic Medicine, Scripps Translational Science Institute, La Jolla, CA, USA
    BMC Genomics 13:508. 2012
    ..The broad range of disease severity may be influenced by bacterial genetic variation...
  73. pmc Association of common genetic variants in GPCPD1 with scaling of visual cortical surface area in humans
    Trygve E Bakken
    Medical Scientist Training Program, University of California at San Diego, La Jolla, CA 92093, USA
    Proc Natl Acad Sci U S A 109:3985-90. 2012
    ..We suggest that identifying genes that contribute to normal cortical architecture provides a first step to understanding genetic mechanisms that underlie visual perception...
  74. pmc The effects of globin on microarray-based gene expression analysis of mouse blood
    Mary E Winn
    Graduate Program in Biomedical Sciences, Department of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
    Mamm Genome 21:268-75. 2010
    ....
  75. doi request reprint DNA sequence-based phenotypic association analysis
    Nicholas J Schork
    Department of Psychiatry, University of California at San Diego, La Jolla, CA 92093, USA
    Adv Genet 60:195-217. 2008
    ..Ultimately, we show that the procedure has promise and argue that consideration of DNA sequence-based association data should usher in a new era in genetic association study designs and methodologies...
  76. ncbi request reprint Accurate prediction of deleterious protein kinase polymorphisms
    Ali Torkamani
    Department of Medicine, Center for Human Genetics and Genomics, The Scripps Research Institute, University of California, San Diego, La Jolla, CA 92093, USA
    Bioinformatics 23:2918-25. 2007
    ..We provide a ranked list of common kinase nsSNPs that have a higher probability of impacting human disease based on our analyses...
  77. pmc Generalized analysis of molecular variance
    Caroline M Nievergelt
    Department of Psychiatry, University of California at San Diego, La Jolla, California, United States of America
    PLoS Genet 3:e51. 2007
    ....
  78. pmc Direct-to-consumer personalized genomic testing
    Cinnamon S Bloss
    Scripps Genomic Medicine, Scripps Health, Scripps Translational Science Institute, 3344 N Torrey Pines Court, La Jolla, CA 92037, USA
    Hum Mol Genet 20:R132-41. 2011
    ..Either way, however, current knowledge needs to be extended and enhanced with respect to the delivery, impact and use of increasingly accurate and comprehensive individualized genomic data...
  79. pmc Genome-wide association of bipolar disorder suggests an enrichment of replicable associations in regions near genes
    Erin N Smith
    Scripps Genomic Medicine and Scripps Translational Science Institute, La Jolla, California, United States of America
    PLoS Genet 7:e1002134. 2011
    ....
  80. pmc Multicenter validation of the diagnostic accuracy of a blood-based gene expression test for assessing obstructive coronary artery disease in nondiabetic patients
    Steven Rosenberg
    CardioDx, Palo Alto, California, USA
    Ann Intern Med 153:425-34. 2010
    ..Previous studies have suggested that peripheral blood gene expression can indicate the presence of CAD...
  81. ncbi request reprint Gene expression in mouse brain following chronic hypoxia: role of sarcospan in glial cell death
    Dan Zhou
    Department of Pediatrics Section of Respiratory Medicine and Neuroscience, University of California San Diego, La Jolla, CA 92093 0735, USA
    Physiol Genomics 32:370-9. 2008
    ..We conclude that CIH or CCH induced significant and distinguishable alterations in gene expression in cortex and hippocampus and that Sspn seems to play a critical role in inducing cell death under hypoxic conditions...
  82. pmc Effect of direct-to-consumer genomewide profiling to assess disease risk
    Cinnamon S Bloss
    Scripps Genomic Medicine, Scripps Translational Science Institute, and Scripps Health, La Jolla, CA 92037, USA
    N Engl J Med 364:524-34. 2011
    ..We examined the psychological, behavioral, and clinical effects of risk scanning with the Navigenics Health Compass, a commercially available test of uncertain clinical validity and utility...
  83. pmc Predicting functional regulatory polymorphisms
    Ali Torkamani
    Department of Molecular and Experimental Medicine, Scripps Genomic Medicine and the Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, CA 92037, USA
    Bioinformatics 24:1787-92. 2008
    ....
  84. pmc Advances in endophenotyping schizophrenia
    David L Braff
    Department of Psychiatry, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0804, USA
    World Psychiatry 7:11-8. 2008
    ..By identifying the single nucleotide polymorphisms (SNPs) associated with endophenotypes in schizophrenia, psychiatric neuroscientists can select new strong inference based molecular targets for the treatment of schizophrenia...
  85. ncbi request reprint Human response to alpha2-adrenergic agonist stimulation studied in an isolated vascular bed in vivo: Biphasic influence of dose, age, gender, and receptor genotype
    Danuta King
    Department of Medicine and Center for Molecular Genetics 0838, University of California at San Diego, and VA San Diego Healthcare System, 9500 Gilman Dr, La Jolla, CA 92093 0838, USA
    Clin Pharmacol Ther 77:388-403. 2005
    ....
  86. ncbi request reprint Admixture mapping as a gene discovery approach for complex human traits and diseases
    Caroline M Nievergelt
    Polymorphism Research Laboratory, Department of Psychiatry, University of California at San Diego, 2050 Basic Science Building, 9500 Gilman Drive, La Jolla, CA 92093 0603, USA
    Curr Hypertens Rep 7:31-7. 2005
    ..We conclude that AM has potential in the identification of disease-predisposing loci, but this potential may only exist in a limited number of realistic settings...
  87. pmc CCCTC-binding factor (CTCF) and cohesin influence the genomic architecture of the Igh locus and antisense transcription in pro-B cells
    Stephanie C Degner
    Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
    Proc Natl Acad Sci U S A 108:9566-71. 2011
    ..Together, our findings demonstrate that CTCF plays an important role in the 3D structure of the Igh locus and in the regulation of antisense germline transcription and that it contributes to the compaction of the Igh locus...
  88. pmc Large-scale integration of human genetic and physical maps
    Caroline M Nievergelt
    Polymorphism Research Laboratory, Department of Psychiatry, University of California at San Diego, La Jolla, California 92093 0603, USA
    Genome Res 14:1199-205. 2004
    ..Our efforts resulted in updated sex-specific genetic maps...
  89. pmc Power calculations for genetic association studies using estimated probability distributions
    Nicholas J Schork
    Department of Psychiatry, University of California at San Diego, 2062 Basic Science Building, 9500 Gilman Drive, La Jolla, CA 92093, USA
    Am J Hum Genet 70:1480-9. 2002
    ....
  90. pmc Identification of rare cancer driver mutations by network reconstruction
    Ali Torkamani
    The Scripps Translational Science Institute and Scripps Genomic Medicine, Scripps Health and The Scripps Research Institute, La Jolla, California 92037, USA
    Genome Res 19:1570-8. 2009
    ....
  91. pmc Contemporary human genetic strategies in aging research
    Cinnamon S Bloss
    Scripps Translational Science Institute and Scripps Health, La Jolla, CA 92037, USA
    Ageing Res Rev 10:191-200. 2011
    ....
  92. pmc Efficient and cost effective population resequencing by pooling and in-solution hybridization
    Vikas Bansal
    Scripps Genomic Medicine, Scripps Translational Science Institute, La Jolla, California, United States of America
    PLoS ONE 6:e18353. 2011
    ..6% of variants below 5% in frequency. Finally, allele frequencies for single nucleotide variants (SNVs) estimated from the pooled data and the HapMap genotype data were tightly correlated (correlation coefficient >  =  0.995)...
  93. ncbi request reprint Evaluation of linkage disequilibrium between chromosome 22q11 single nucleotide polymorphisms in a large outbred population
    Sarah H Shaw
    Axys Pharmaceuticals Inc, La Jolla, California, USA
    Am J Med Genet 114:205-13. 2002
    ..30. Finally, we observed a 60 kb region with non-significant LD, which could reflect increased recombination in this region...
  94. pmc Prestige centrality-based functional outlier detection in gene expression analysis
    Ali Torkamani
    The Scripps Translational Science Institute and Scripps Genomic Medicine, Scripps Health and The Scripps Research Institute, 3344 North Torrey Pines Court, Room 306 La Jolla, CA 92037 USA
    Bioinformatics 25:2222-8. 2009
    ..This situation is likely to occur in single cell gene expression experiments or in noisy experimental settings where a small sub-population of cells contributes to the gene expression signature of interest...
  95. ncbi request reprint Susceptibility and modifier genes in Portuguese transthyretin V30M amyloid polyneuropathy: complexity in a single-gene disease
    Miguel L Soares
    Department of Molecular and Experimental Medicine, Division of Rheumatology Research and the WM Keck Autoimmune Disease Center, The Scripps Research Institute, La Jolla, CA 92037, USA
    Hum Mol Genet 14:543-53. 2005
    ..Thus, although the TTR V30M mutation is required for the disease in Portuguese patients, different genetic factors may govern the age of onset, as well as the occurrence of anticipation...
  96. pmc Multivariate regression analysis of distance matrices for testing associations between gene expression patterns and related variables
    Matthew A Zapala
    Biomedical Sciences Graduate Program and the Polymorphism Research Laboratory, Department of Psychiatry, Moores UCSD Cancer Center, Center for Human Genetics and Genomics, University of California at San Diego, La Jolla, CA 92093, USA
    Proc Natl Acad Sci U S A 103:19430-5. 2006
    ..We showcase the methodology using three published gene expression data sets...
  97. ncbi request reprint A polymorphism of the beta1-adrenergic receptor is associated with low extraversion
    Murray B Stein
    Department of Psychiatry, University of California San Diego, San Diego, California, USA
    Biol Psychiatry 56:217-24. 2004
    ..We examined the possibility that allelic variation leading to alterations in beta(1)-adrenergic function might be present in persons with elevated social anxiety-related traits...
  98. ncbi request reprint Distribution analysis of nonsynonymous polymorphisms within the human kinase gene family
    Ali Torkamani
    Graduate Program in Biomedical Sciences, Department of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
    Genomics 90:49-58. 2007
    ..Our results provide insights into the sequence and structural phenomena associated with naturally occurring kinase nscSNPs that contribute to human diseases...
  99. ncbi request reprint A new framework marker-based linkage map and SDPs for the rat HXB/BXH strain set
    Martin Jirout
    Department of Pharmacology 0636, University of California San Diego, La Jolla, California 92093 0636, USA
    Mamm Genome 14:537-46. 2003
    ..The new genotypic information obtained also permitted further genetic characterization of the RI strain set including strain independence, genetic similarity among the individual strains, and non-syntenic associations between loci...

Research Grants2

  1. FAMILY BLOOD PRESSURE PROGRAM
    Nicholas Schork; Fiscal Year: 2004
    ..The resulting synthesis of ideas and amassed data permits rigorous hypothesis testing not otherwise possible and will hasten understanding of the previously elusive genetic variation responsible for disease risk. ..