Genomes and Genes
Affiliation: University of California
- Evidence of novel fine-scale structural variation at autism spectrum disorder candidate lociDale J Hedges
Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10 Ave, M 860, Miami, FL 33136, USA
Mol Autism 3:2. 2012..abstract:..
- Genetic variation in the odorant receptors family 13 and the mhc loci influence mate selection in a multiple sclerosis datasetPouya Khankhanian
Department of Neurology, University of California, San Francisco, CA 94143 0435, USA
BMC Genomics 11:626. 2010..Attempts at replication of these genetic results in human studies, however, have reached conflicting conclusions...
- The molecular signature of therapeutic mesenchymal stem cells exposes the architecture of the hematopoietic stem cell niche synapseEnrico Pedemonte
Department of Neurology, School of Medicine, University of California, San Francisco, CA, USA
BMC Genomics 8:65. 2007....
- SNPs in Multi-species Conserved Sequences (MCS) as useful markers in association studies: a practical approachJacob L McCauley
Center for Human Genetics Research and Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN, USA
BMC Genomics 8:266. 2007..We chose annotated SNPs in the region based on location within MCSs (termed MCS-SNPs). We then obtained genotypes for 478 MCS-SNPs in 989 individuals from MS families...
- Copy number variation in African AmericansJoseph P McElroy
Department of Neurology, University of California, San Francisco, CA, USA
BMC Genet 10:15. 2009..It is important, therefore, to understand the distribution of CNVs within and among populations. This study is the first report of a CNV map in African Americans...
- Multiple sclerosis genetics--is the glass half full, or half empty?Jorge R Oksenberg
Department of Neurology, School of Medicine, University of California at San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143 0435, USA
Nat Rev Neurol 6:429-37. 2010..This Review briefly summarizes well-established concepts of MS epidemiology and susceptibility, and discusses new knowledge emerging from genome-wide association studies...
- Modeling the cumulative genetic risk for multiple sclerosis from genome-wide association dataJoanne H Wang
Department of Neurology, University of California San Francisco, San Francisco, CA 94143 0435, USA
Genome Med 3:3. 2011..Nevertheless, the knowledge of MS genetics remains incomplete, with many risk alleles still to be revealed...
- The genetics of multiple sclerosis: SNPs to pathways to pathogenesisJorge R Oksenberg
Department of Neurology, School of Medicine, University of California at San Francisco, 513 Parnassus Avenue, San Francisco, California 94143 0435, USA
Nat Rev Genet 9:516-26. 2008....
- Risk alleles for multiple sclerosis identified by a genomewide studyDavid A Hafler
Division of Molecular Immunology, Center for Neurologic Diseases, Department of Neurology, Brigham and Women s Hospital, and Harvard Medical School, Boston, USA
N Engl J Med 357:851-62. 2007..Multiple sclerosis has a clinically significant heritable component. We conducted a genomewide association study to identify alleles associated with the risk of multiple sclerosis...
- Linkage and association with the NOS2A locus on chromosome 17q11 in multiple sclerosisLisa F Barcellos
Department of Neurology, School of Medicine, University of California at San Francisco, San Francisco, CA 94143 0435, USA
Ann Neurol 55:793-800. 2004..Our results provide strong evidence for linkage and association to a new candidate disease gene on chromosome 17q11 in MS and suggest that variation within NOS2A or a nearby locus contributes to disease susceptibility...
- Increased transcriptional activity of milk-related genes following the active phase of experimental autoimmune encephalomyelitis and multiple sclerosisDavid Otaegui
University of California San Francisco, San Francisco, CA 94143, USA
J Immunol 179:4074-82. 2007..The potential role of lactogenic hormones in MS is discussed...
- Heterogeneity at the HLA-DRB1 locus and risk for multiple sclerosisLisa F Barcellos
Division of Epidemiology, School of Public Health, University of California, Berkeley 94720, USA, and Department of Clinical Neurosciences, University of Cambridge, Addenbrooke s Hospital, UK
Hum Mol Genet 15:2813-24. 2006....
- Conferral of enhanced natural killer cell function by KIR3DS1 in early human immunodeficiency virus type 1 infectionBrian R Long
Division of Experimental Medicine, Department of Medicine, San Francisco General Hospital, University of California, San Francisco, USA
J Virol 82:4785-92. 2008....
- Uncoupling the roles of HLA-DRB1 and HLA-DRB5 genes in multiple sclerosisStacy J Caillier
Department of Neurology, University of California, San Francisco, CA 94143, USA
J Immunol 181:5473-80. 2008..The data underscore the power of the African American MS dataset to identify disease genes by association in a region of high linkage disequilibrium...
- Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosisSergio E Baranzini
Department of Neurology, University of California, San Francisco, CA 94143 0435, USA
Hum Mol Genet 18:767-78. 2009..Gene ontology-based analysis shows a functional dichotomy between genes involved in the susceptibility pathway and those affecting the clinical phenotype...
- Meta-analysis of genome scans and replication identify CD6, IRF8 and TNFRSF1A as new multiple sclerosis susceptibility lociPhilip L De Jager
Division of Molecular Immunology, Center for Neurologic Diseases, Department of Neurology, Brigham and Women s Hospital and Harvard Medical School, Boston, MA, USA
Nat Genet 41:776-82. 2009....
- Synergy or independence? Deciphering the interaction of HLA Class I and NK cell KIR alleles in early HIV-1 disease progressionJason D Barbour
HIV AIDS Division, Department of Medicine, San Francisco General Hospital, University of California San Francisco, San Francisco, California, United States of America
PLoS Pathog 3:e43. 2007
- Genetic variation influences glutamate concentrations in brains of patients with multiple sclerosisSergio E Baranzini
Department of Neurology, School of Medicine, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143 0435, USA
Brain 133:2603-11. 2010..Spectroscopy-based imaging provides a novel quantitative endophenotype for genetic association studies directed towards identifying new factors that contribute to the heterogeneity of clinical expression of multiple sclerosis...
- Genome-wide pharmacogenomic analysis of the response to interferon beta therapy in multiple sclerosisEsther Byun
Department of Neurology, University of California, San Francisco, San Francisco, CA 94143 0435, USA
Arch Neurol 65:337-44. 2008..Recombinant interferon beta therapy is widely used to reduce disease activity in multiple sclerosis (MS). However, up to 50% of patients continue to have relapses and worsening disability despite therapy...
- Pathway and network-based analysis of genome-wide association studies in multiple sclerosisSergio E Baranzini
Department of Neurology, School of Medicine, University of California San Francisco, 513 Parnassus Ave Room S 256, San Francisco, CA 94143 0435, USA
Hum Mol Genet 18:2078-90. 2009..In addition to the immunological pathways previously identified, we report here for the first time the potential involvement of neural pathways in MS susceptibility...
- CIITA variation in the presence of HLA-DRB1*1501 increases risk for multiple sclerosisPaola G Bronson
Genetic Epidemiology and Genomics Laboratory, Division of Epidemiology, School of Public Health, University of California, Berkeley, CA 94720 7356, USA
Hum Mol Genet 19:2331-40. 2010..15-1.95, P = 2.3 x 10(-3)) of CLEC16A rs6498169*G, a putative MS risk allele adjacent to CIITA. Our results provide strong evidence supporting a role for CIITA variation in MS risk, which appears to depend on the presence of DRB1*1501...
- Gene expression analysis reveals altered brain transcription of glutamate receptors and inflammatory genes in a patient with chronic focal (Rasmussen's) encephalitisSergio E Baranzini
Department of Neurology, University of California at San Francisco, 513 Parnassus Avenue, S 256, San Francisco, CA 94143 0435, USA
J Neuroimmunol 128:9-15. 2002..e. IL1 beta, IgVH, and IL2R gamma among others) and a striking down-regulation of several GluRs, in particular mGluR4. This type of analysis may prove useful in describing the molecular events underlying intractable epilepsy...
- Refining the association of MHC with multiple sclerosis in African AmericansJoseph P McElroy
Department of Neurology, University of California, San Francisco, CA 94143, USA
Hum Mol Genet 19:3080-8. 2010....
- Mapping multiple sclerosis susceptibility to the HLA-DR locus in African AmericansJorge R Oksenberg
Department of Neurology, University of California at San Francisco, San Francisco, CA 94143 0435, USA
Am J Hum Genet 74:160-7. 2004..This finding is unlikely to be solely explained by admixture, since a substantial proportion of the susceptibility chromosomes from African American patients with MS displayed haplotypes consistent with an African origin...
- A major histocompatibility Class I locus contributes to multiple sclerosis susceptibility independently from HLA-DRB1*15:01Bruce A C Cree
Department of Neurology, University of California San Francisco, San Francisco, California, United States of America
PLoS ONE 5:e11296. 2010..Whether other major histocompatibility complex (MHC) genes contribute to MS susceptibility is controversial...
- Vitamin D status is associated with relapse rate in pediatric-onset multiple sclerosisEllen M Mowry
MS Center, Department of Neurology, University of California, San Francisco, San Francisco, CA 94117, USA
Ann Neurol 67:618-24. 2010..We sought to determine if vitamin D status, a risk factor for multiple sclerosis, is associated with the rate of subsequent clinical relapses in pediatric-onset multiple sclerosis...
- Genome, epigenome and RNA sequences of monozygotic twins discordant for multiple sclerosisSergio E Baranzini
Department of Neurology, University of California at San Francisco, San Francisco, California 94143, USA
Nature 464:1351-6. 2010..These are the first, to our knowledge, female, twin and autoimmune disease individual genome sequences reported...
- Transcription-based prediction of response to IFNbeta using supervised computational methodsSergio E Baranzini
Department of Neurology, School of Medicine University of California, San Francisco, USA
PLoS Biol 3:e2. 2005..Large-scale kinetic reverse-transcription PCR, coupled with advanced data-mining efforts, can effectively reveal preexisting and drug-induced gene expression signatures associated with therapeutic effects...
- Modification of Multiple Sclerosis Phenotypes by African Ancestry at HLABruce A C Cree
Department of Neurology, University of California San Francisco, USA
Arch Neurol 66:226-33. 2009....
- Modular transcriptional activity characterizes the initiation and progression of autoimmune encephalomyelitisSergio E Baranzini
Department of Neurology, School of Medicine, University of California, San Francisco, 94143, USA
J Immunol 174:7412-22. 2005..Our study demonstrates the utility of large-scale transcriptional studies and advanced data mining to decipher complex biological processes such as those involved in MS and other neurodegenerative disorders...
- Genetics of multiple sclerosisJorge R Oksenberg
Department of Neurology, University of California at San Francisco, School of Medicine, 513 Parnassus Avenue S-256, San Francisco, CA 94143-0435, USA
Neurol Clin 23:61-75, vi. 2005
- Variation within DNA repair pathway genes and risk of multiple sclerosisFarren B S Briggs
University of California, Berkeley, 94720, USA
Am J Epidemiol 172:217-24. 2010..Although other candidate genes examined here warrant further follow-up studies, collectively, these results derived from a well-powered study do not support a strong role for common variation within DNA repair pathway genes in MS...
- Abrogation of T cell quiescence characterizes patients at high risk for multiple sclerosis after the initial neurological eventJean Christophe Corvol
Departments of Neurology and Radiology, University of California, San Francisco, CA 94143 0435, USA
Proc Natl Acad Sci U S A 105:11839-44. 2008..These results indicate that CIS patients at high risk of conversion have impaired regulation of T cell quiescence, possibly resulting in earlier activation of pathogenic CD4(+) cells...
- Genomics and new targets for multiple sclerosisSergio E Baranzini
University of California, Department of Neurology, School of Medicine, San Francisco, CA 94143-0435, USA
Pharmacogenomics 6:151-61. 2005..Equally significant, it is likely that locus heterogeneity exists, whereby specific genes influence susceptibility and pathogenesis in some individuals but not in others...
- Clustering of autoimmune diseases in families with a high-risk for multiple sclerosis: a descriptive studyLisa F Barcellos
School of Public Health, Division of Epidemiology, University of California, Berkeley, CA, USA
Lancet Neurol 5:924-31. 2006..This distinct multiple-sclerosis phenotype, defined by its association with other autoimmune diseases, segregates with specific genotypes that could underlie the common susceptibility...
- Mapping gene activity in complex disorders: Integration of expression and genomic scans for multiple sclerosisGuy Haskin Fernald
Department of Neurology, School of Medicine, University of California, 513 Parnassus Avenue, S-256, San Francisco, CA 94143-0435, USA
J Neuroimmunol 167:157-69. 2005..Integration of genomic and transcriptional information is a powerful tool to dissect genetic susceptibility in complex multifactorial disorders like MS...
- Genome-wide network analysis reveals the global properties of IFN-beta immediate transcriptional effects in humansGuy Haskin Fernald
School of Medicine, University of California, San Francisco, CA 94143, USA
J Immunol 178:5076-85. 2007..Implications of this method in the creation of personalized models of response to therapy are discussed...
- New insights into the genetics of multiple sclerosisSergio E Baranzini
Department of Neurology, San Francisco School of Medicine, University of California, 94143, USA
J Rehabil Res Dev 39:201-9. 2002..The identification and characterization of the genes are likely to define the basic etiology of the disease, improve risk assessment, and influence therapeutics...
- Differential impact of the CD45 juxtamembrane wedge on central and peripheral T cell receptor responsesMichelle L Hermiston
Department of Pediatrics, Medicine, Howard Hughes Medical Institute, University of California, San Francisco, CA 94143, USA
Proc Natl Acad Sci U S A 106:546-51. 2009..Together, the data support a role for the CD45 wedge in regulation of T cell responses in vivo and suggest that its effects depend on cellular context...
- The neurobiology of multiple sclerosis: genes, inflammation, and neurodegenerationStephen L Hauser
Department of Neurology, School of Medicine, University of California at San Francisco, San Francisco, California 94143, USA
Neuron 52:61-76. 2006..Together, these advances have set the stage for the development of therapeutic approaches designed to target the demyelinating and neurodegenerative components of the disease and promote repair...
- Investigation of seven proposed regions of linkage in multiple sclerosis: an American and French collaborative studyMargaret A Pericak-Vance
Center for Human Genetics, Duke University Medical Center, Durham, North Carolina, USA
Neurogenetics 5:45-8. 2004..Regions on 1p34, 3p14, and 19q13 produced lod scores >0.90 in at least one subset of the data, suggesting that these regions should be examined in more detail...
- Fine-mapping the genetic basis of CRP regulation in African Americans: a Bayesian approachBenjamin Rhodes
Section of Molecular Genetics and Rheumatology, Faculty of Medicine, Imperial College, Du Cane Road, London W12 0NN, UK
Hum Genet 123:633-42. 2008....
- Neurogenetics in the Annals: dealing with complexityJorge R Oksenberg
Ann Neurol 63:A11-4. 2008
- Gene-microarray analysis of multiple sclerosis lesions yields new targets validated in autoimmune encephalomyelitisChristopher Lock
Department of Neurology and Neurological Sciences, Beckman Center, Stanford University, Stanford, California, USA
Nat Med 8:500-8. 2002..These results in EAE corroborate the microarray studies on MS lesions. Large-scale analysis of transcripts in MS lesions elucidates new aspects of pathology and opens possibilities for therapy...
- Multiple sclerosis: deeper understanding of its pathogenesis reveals new targets for therapyLawrence Steinman
Department of Neurology and Neurological Sciences, Stanford University School of Medicine, California 94305, USA
Annu Rev Neurosci 25:491-505. 2002..Some of these participants may be useful targets for therapy...
- The HLA locus and multiple sclerosis in Spain. Role in disease susceptibility, clinical course and response to interferon-betaPablo Villoslada
Neuroimmunology Unit, Hospital Vall d'Hebron, Barcelona, Spain
J Neuroimmunol 130:194-201. 2002..Similarly, no difference in the distribution of responders and nonresponders to interferon-beta (IFNB) therapy, as defined by primary and secondary end points, was observed when individuals were stratified according to HLA-DR2 status...
- Methods for high-density admixture mapping of disease genesNick Patterson
Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
Am J Hum Genet 74:979-1000. 2004..A particularly important result is that the power of an admixture mapping study to detect a locus will be nearly the same for a wide range of mixture scenarios: the mixture proportion should be 10%-90% from both ancestral populations...
- Enhancing linkage analysis of complex disorders: an evaluation of high-density genotypingStephen J Sawcer
University of Cambridge Neurology Unit, Addenbrooke s Hospital, UK
Hum Mol Genet 13:1943-9. 2004..The extent of additional information extracted is considerable, indicating that reanalysis of existing multiplex families using these newer systems would substantially increase power...
- A high-density screen for linkage in multiple sclerosisStephen Sawcer
University of Cambridge, Department of Clinical Neuroscience, Addenbrooke s Hospital, Hills Road, Cambridge, CB2 2QQ, United Kingdom
Am J Hum Genet 77:454-67. 2005....
- A whole-genome admixture scan finds a candidate locus for multiple sclerosis susceptibilityDavid Reich
Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
Nat Genet 37:1113-8. 2005..We describe here the first high-powered admixture scan, focusing on 605 African American cases and 1,043 African American controls, and report a locus on chromosome 1 that is significantly associated with multiple sclerosis...
- Association of the truncating splice site mutation in BTNL2 with multiple sclerosis is secondary to HLA-DRB1*15James A Traherne
Cambridge Institute for Medical Research, Wellcome Trust MRC Building, Cambridge, UK
Hum Mol Genet 15:155-61. 2006..The association of BTNL2 with MS observed in the African-American data set was also secondary to the primary DRB1*15 association...
- Association of polymorphisms in the apolipoprotein E region with susceptibility to and progression of multiple sclerosisSilke Schmidt
Center for Human Genetics, Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
Am J Hum Genet 70:708-17. 2002..03), whereas a higher proportion of APOE-2 carriers exhibit a mild disease course (P=.02)...
- A second major histocompatibility complex susceptibility locus for multiple sclerosisTai Wai Yeo
Department of Clinical Neurosciences, University of Cambridge, Addenbrooke s Hospital, Cambridge, United Kingdom
Ann Neurol 61:228-36. 2007..The possibility that other genes in the MHC independently influence susceptibility to multiple sclerosis has been suggested but remains unconfirmed...
- Evidence for association of chromosome 10 open reading frame (C10orf27) gene polymorphisms and multiple sclerosisRobert Goertsches
Unitat de Neuroimmunologia Clinica, Hospital Universitari Vall d Hebron HUVH, 08035 Barcelona, Spain
Mult Scler 14:412-4. 2008..Transcript expression in brain lesions from MS patients was increased. These findings suggest C10orf27 as a candidate gene for MS susceptibility and pathogenesis...
- Interleukin 7 receptor alpha chain (IL7R) shows allelic and functional association with multiple sclerosisSimon G Gregory
Center for Human Genetics, Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
Nat Genet 39:1083-91. 2007..The SNP influences the amount of soluble and membrane-bound isoforms of the protein by putatively disrupting an exonic splicing silencer...
- The autoimmune disease-associated IL12B and IL23R polymorphisms in multiple sclerosisAnn B Begovich
Celera, Alameda, CA, USA
Hum Immunol 68:934-7. 2007..Family-based association analysis was performed. There was no evidence of transmission distortion of any of the tested alleles in this data set...
- Quantitative longitudinal analysis of T cell receptor repertoire expression in HIV-infected patients on antiretroviral and interleukin-2 therapyUma Sriram
Department of Neurology University of California at San Francisco, California 94143, USA
AIDS Res Hum Retroviruses 23:741-7. 2007..These results suggest that homeostasis in the T cell receptor repertoire is more robust in those patients who stay on HAART for a long time and confirm the polyclonal stimulating capacity of IL-2...
- The Population Reference Sample, POPRES: a resource for population, disease, and pharmacological genetics researchMatthew R Nelson
GlaxoSmithKline, Research Triangle Park, NC 27709, USA
Am J Hum Genet 83:347-58. 2008..The genotype and demographic data from this reference sample are freely available through the NCBI database of Genotypes and Phenotypes (dbGaP)...
- Multiple susceptibility loci for multiple sclerosisJonathan L Haines
Program in Human Genetics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
Hum Mol Genet 11:2251-6. 2002..These regions can now be targeted for detailed study to identify the underlying MS susceptibility genes...
- Chromosome 7q21-22 and multiple sclerosisPablo Villoslada
J Neuroimmunol 150:1-2. 2004
- Re: GAMES issueJorge R Oksenberg
J Neuroimmunol 153:1-2. 2004
- The R620W polymorphism of the protein tyrosine phosphatase PTPN22 is not associated with multiple sclerosisAnn B Begovich
Am J Hum Genet 76:184-7. 2005
- Complex gene-gene interactions in multiple sclerosis: a multifactorial approach reveals associations with inflammatory genesAlison A Motsinger
Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, 519 Light Hall, Vanderbilt University Medical School, Nashville, TN 37232 0700, USA
Neurogenetics 8:11-20. 2007..These results suggest that significant epistasis, or gene-gene interactions, may exist even in the absence of statistically significant individual main effects...
- Immunogenetic Studies in Multiple SclerosisJorge Oksenberg; Fiscal Year: 2006..abstract_text> ..
- Immunomodulation in Multiple Sclerosis by Interferon BJorge Oksenberg; Fiscal Year: 2005..In addition to new insights into the fundamental biology of interferons, our results will potentially identify surrogate markers of activity, and define the molecular basis of interferon response heterogeneity. ..
- Immunogenetic Studies in Multiple SclerosisJorge R Oksenberg; Fiscal Year: 2010..Their identification will help to define the basic etiology of MS, improve risk assessment, and influence therapeutics. ..