STEPHEN J O'BRIEN

Summary

Affiliation: National Cancer Institute
Country: USA

Publications

  1. ncbi The evolution of cats. Genomic paw prints in the DNA of the world's wild cats have clarified the cat family tree and uncovered several remarkable migrations in their past
    STEPHEN J O'BRIEN
    Laboratory of Genomic Diversity, National Cancer Institute, USA
    Sci Am 297:68-75. 2007
  2. pmc Genetic characterization of feline leukemia virus from Florida panthers
    Meredith A Brown
    National Cancer Institute, Frederick, Maryland, USA
    Emerg Infect Dis 14:252-9. 2008
  3. ncbi Applying molecular genetic tools to the conservation and action plan for the critically endangered Far Eastern leopard (Panthera pardus orientalis)
    Olga Uphyrkina
    Laboratory of Evolutionary Zoology and Genetics, Institute of Biology and Soil Sciences, Russian Academy of Sciences, Vladivostok, 690022, Russia
    C R Biol 326:S93-7. 2003
  4. pmc Functions, structure, and read-through alternative splicing of feline APOBEC3 genes
    Carsten Munk
    Division of Medical Biotechnology, Paul Ehrlich Institut, 63225 Langen, Germany
    Genome Biol 9:R48. 2008
  5. pmc A population-based study to investigate host genetic factors associated with hepatitis B infection and pathogenesis in the Chinese population
    Zheng Zeng
    SAIC Laboratory of Genomic Diversity, National Cancer Institute Frederick, National Institutes of Health, Frederick, USA
    BMC Infect Dis 8:1. 2008
  6. pmc The adaptive evolution of the mammalian mitochondrial genome
    Rute R da Fonseca
    REQUIMTE, Departamento de Quimica, Faculdade de Ciencias, Universidade do Porto, Rua do Campo Alegre, 687, 4169 007 Porto, Portugal
    BMC Genomics 9:119. 2008
  7. pmc Light whole genome sequence for SNP discovery across domestic cat breeds
    James C Mullikin
    Genome Technology Branch and NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    BMC Genomics 11:406. 2010
  8. pmc Genomic organization, sequence divergence, and recombination of feline immunodeficiency virus from lions in the wild
    Jill Pecon-Slattery
    Laboratory of Genomic Diversity, National Cancer Institute Frederick, Frederick MD 21702 USA
    BMC Genomics 9:66. 2008
  9. pmc Accounting for multiple comparisons in a genome-wide association study (GWAS)
    Randall C Johnson
    Basic Research Program, SAIC Frederick, Inc NCI Frederick, Frederick, MD, USA
    BMC Genomics 11:724. 2010
  10. pmc Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary
    Johannes Krause
    Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D 04103 Leipzig, Germany
    BMC Evol Biol 8:220. 2008

Detail Information

Publications99

  1. ncbi The evolution of cats. Genomic paw prints in the DNA of the world's wild cats have clarified the cat family tree and uncovered several remarkable migrations in their past
    STEPHEN J O'BRIEN
    Laboratory of Genomic Diversity, National Cancer Institute, USA
    Sci Am 297:68-75. 2007
  2. pmc Genetic characterization of feline leukemia virus from Florida panthers
    Meredith A Brown
    National Cancer Institute, Frederick, Maryland, USA
    Emerg Infect Dis 14:252-9. 2008
    ..These unique features may also account for the severity of the outbreak after cross-species transmission to the panther...
  3. ncbi Applying molecular genetic tools to the conservation and action plan for the critically endangered Far Eastern leopard (Panthera pardus orientalis)
    Olga Uphyrkina
    Laboratory of Evolutionary Zoology and Genetics, Institute of Biology and Soil Sciences, Russian Academy of Sciences, Vladivostok, 690022, Russia
    C R Biol 326:S93-7. 2003
    ..The genetic status and implication for conservation management of the Far Eastern leopard subspecies are discussed...
  4. pmc Functions, structure, and read-through alternative splicing of feline APOBEC3 genes
    Carsten Munk
    Division of Medical Biotechnology, Paul Ehrlich Institut, 63225 Langen, Germany
    Genome Biol 9:R48. 2008
    ..While primates encode seven of these genes (A3A to A3H), rodents carry only a single A3 gene...
  5. pmc A population-based study to investigate host genetic factors associated with hepatitis B infection and pathogenesis in the Chinese population
    Zheng Zeng
    SAIC Laboratory of Genomic Diversity, National Cancer Institute Frederick, National Institutes of Health, Frederick, USA
    BMC Infect Dis 8:1. 2008
    ..We believe that a better understanding of these factors and interactions will lead to more effective diagnostic and therapeutic options...
  6. pmc The adaptive evolution of the mammalian mitochondrial genome
    Rute R da Fonseca
    REQUIMTE, Departamento de Quimica, Faculdade de Ciencias, Universidade do Porto, Rua do Campo Alegre, 687, 4169 007 Porto, Portugal
    BMC Genomics 9:119. 2008
    ....
  7. pmc Light whole genome sequence for SNP discovery across domestic cat breeds
    James C Mullikin
    Genome Technology Branch and NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    BMC Genomics 11:406. 2010
    ..However, to realize this bio-medical potential, a high density single nucleotide polymorphism (SNP) map is required in order to accomplish disease and phenotype association discovery...
  8. pmc Genomic organization, sequence divergence, and recombination of feline immunodeficiency virus from lions in the wild
    Jill Pecon-Slattery
    Laboratory of Genomic Diversity, National Cancer Institute Frederick, Frederick MD 21702 USA
    BMC Genomics 9:66. 2008
    ..In African lions (Panthera leo) and other exotic felid species, disease etiology introduced by FIV infection are less clear, but recent studies indicate that FIV causes moderate to severe CD4 depletion...
  9. pmc Accounting for multiple comparisons in a genome-wide association study (GWAS)
    Randall C Johnson
    Basic Research Program, SAIC Frederick, Inc NCI Frederick, Frederick, MD, USA
    BMC Genomics 11:724. 2010
    ..We consider seven implementations of these commonly used methods using data from 1514 European American participants genotyped for 700,078 SNPs in a GWAS for AIDS...
  10. pmc Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary
    Johannes Krause
    Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D 04103 Leipzig, Germany
    BMC Evol Biol 8:220. 2008
    ..Widely divergent topologies have been suggested based on various data sets and methods...
  11. ncbi Comparative genomics: lessons from cats
    S J O'Brien
    Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702 1201, USA
    Trends Genet 13:393-9. 1997
    ..We review here the remarkable extent of genome homology conservation among mammals illustrated by technology applications in the feline genome project...
  12. doi State of cat genomics
    STEPHEN J O'BRIEN
    Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702, USA
    Trends Genet 24:268-79. 2008
    ..We review these recent advances here. As the genome resources develop, the cat is poised to make a major contribution to many areas in genetics and biology...
  13. ncbi The platypus genome unraveled
    STEPHEN J O'BRIEN
    Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702 1201, USA
    Cell 133:953-5. 2008
    ..The genome of the platypus has been sequenced, assembled, and annotated by an international genomics team. Like the animal itself the platypus genome contains an amalgam of mammal, reptile, and bird-like features...
  14. ncbi Big cat genomics
    STEPHEN J O'BRIEN
    Laboratory of Genomic Diversity, National Cancer Institute, Frederick, Maryland 21702, USA
    Annu Rev Genomics Hum Genet 6:407-29. 2005
    ..Conservation, stabilization, and management of the big cats are important areas that derive benefit from the genome resources expanded and applied to highly successful species, imperiled by an expanding human population...
  15. ncbi Human genes that limit AIDS
    STEPHEN J O'BRIEN
    Laboratory of Genomic Diversity, National Cancer Institute, Frederick, Maryland, USA
    Nat Genet 36:565-74. 2004
    ..The influence and translational impact of these genes on individual and population sensitivity to AIDS is considerable...
  16. ncbi Polygenic and multifactorial disease gene association in man: Lessons from AIDS
    S J O'Brien
    Laboratory of Genomic Diversity, National Cancer Institute, Intramural Research Support Program, SAIC Frederick, National Cancer Institute Frederick Cancer Research and Development Center, Frederick, Maryland 21702 1201, USA
    Annu Rev Genet 34:563-591. 2000
    ....
  17. ncbi Stewardship of human biospecimens, DNA, genotype, and clinical data in the GWAS era
    STEPHEN J O'BRIEN
    Laboratory of Genomic Diversity, National Cancer Institute, Frederick, Maryland 21702 1201, USA
    Annu Rev Genomics Hum Genet 10:193-209. 2009
    ..A way forward may be to convene a colloquium of international medical and science organizations charged with developing global consensus guidance and ethical principles for access to and use of genomic biobanks...
  18. ncbi The Feline Genome Project
    STEPHEN J O'BRIEN
    Laboratory of Genomic Diversity, National Cancer Institute Frederick, Frederick, Maryland 21702 1201, USA
    Annu Rev Genet 36:657-86. 2002
    ..Here we review the advantages, rationale, and present strategy of a feline genome project, and we describe the disease models, comparative genomics, and biological applications posed by the full resolution of the cat's genome...
  19. ncbi The effect of genetic variation in chemokines and their receptors on HIV transmission and progression to AIDS
    S J O'Brien
    Laboratory of Genomic Diversity, National Cancer Institute, Frederick, Maryland, USA 21702 1201, USA
    Immunol Rev 177:99-111. 2000
    ..The functional and therapeutic implications of these AIDS restriction genes for disease progression and intervention are explored in this review...
  20. pmc Effect of host genetics on incidence of HIV neuroretinal disorder in patients with AIDS
    Efe Sezgin
    Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702 1201, USA
    J Acquir Immune Defic Syndr 54:343-51. 2010
    ..Clearly, further studies are warrented...
  21. ncbi The late Miocene radiation of modern Felidae: a genetic assessment
    Warren E Johnson
    Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702 1201, USA
    Science 311:73-7. 2006
    ..The phylogenetic performance of distinct gene classes showed that Y-chromosome segments are appreciably more informative than mitochondrial DNA, X-linked, or autosomal genes in resolving the rapid Felidae species radiation...
  22. pmc Phylogeography and genetic ancestry of tigers (Panthera tigris)
    Shu Jin Luo
    Laboratory of Genomic Diversity, National Cancer Institute, Frederick, Maryland, USA
    PLoS Biol 2:e442. 2004
    ..These results provide an explicit basis for subspecies recognition and will lead to the improved management and conservation of these recently isolated but distinct geographic populations of tigers...
  23. pmc Polymorphisms of CUL5 are associated with CD4+ T cell loss in HIV-1 infected individuals
    Ping An
    Laboratory of Genomic Diversity, SAIC Frederick, Incorporated, National Cancer Institute, Frederick, Maryland, United States of America
    PLoS Genet 3:e19. 2007
    ....
  24. pmc Association of host genetic risk factors with the course of cytomegalovirus retinitis in patients infected with human immunodeficiency virus
    Efe Sezgin
    Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702, USA
    Am J Ophthalmol 151:999-1006.e4. 2011
    ....
  25. pmc Genetic factors leading to chronic Epstein-Barr virus infection and nasopharyngeal carcinoma in South East China: study design, methods and feasibility
    Xiu Chan Guo
    Laboratory of Genomic Diversity, SAIC Frederick, National Cancer Institute Frederick, Frederick, MD 21702, USA
    Hum Genomics 2:365-75. 2006
    ....
  26. doi Host genetic influences on highly active antiretroviral therapy efficacy and AIDS-free survival
    Sher L Hendrickson
    Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702 1201, USA
    J Acquir Immune Defic Syndr 48:263-71. 2008
    ..27; P=0.01). ARG influence after HAART suggests residual HIV-1 replication, and spread continues even in patients successfully suppressing detectable viral RNA...
  27. pmc Seroprevalence and genomic divergence of circulating strains of feline immunodeficiency virus among Felidae and Hyaenidae species
    Jennifer L Troyer
    Laboratory of Genomic Diversity, National Cancer Institute Frederick, Maryland 21702 1201, USA
    J Virol 79:8282-94. 2005
    ....
  28. pmc Association of Y chromosome haplogroup I with HIV progression, and HAART outcome
    Efe Sezgin
    NCI Frederick, MD 21702, USA
    Hum Genet 125:281-94. 2009
    ..Our results suggest that one or more loci on the Y chromosome found on haplogroup Y-I have an effect on AIDS progression and treatment responses in European Americans...
  29. pmc A high-density admixture map for disease gene discovery in african americans
    Michael W Smith
    Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD, USA
    Am J Hum Genet 74:1001-13. 2004
    ..The map is especially appropriate for those diseases that differ in incidence between the parental African and European populations...
  30. pmc Genetic variation in the CCL18-CCL3-CCL4 chemokine gene cluster influences HIV Type 1 transmission and AIDS disease progression
    William S Modi
    SAIC Frederick, Inc, Basic Research Program, Frederick, MD 21702 1201, USA
    Am J Hum Genet 79:120-8. 2006
    ..01-.02). These results reiterate the importance of chemokine gene variation in HIV-1/AIDS pathogenesis and emphasize that localized linkage disequilibrium makes the identification of causal mutations difficult...
  31. ncbi MCP-1-MCP-3-Eotaxin gene cluster influences HIV-1 transmission
    William S Modi
    SAIC Frederick and the Laboratory of Genomic Diversity, National Cancer Institute, Frederick, Maryland, USA
    AIDS 17:2357-65. 2003
    ..An epidemiological analysis identified genetic variants influencing HIV-1 transmission and disease progression...
  32. pmc Mitochondrial DNA haplogroups influence AIDS progression
    Sher L Hendrickson
    Laboratory of Genomic Diversity, National Cancer Institute, Frederick, Maryland 21702 1201, USA
    AIDS 22:2429-39. 2008
    ....
  33. pmc Evaluation of IL10, IL19 and IL20 gene polymorphisms and chronic hepatitis B infection outcome
    Ann L Truelove
    Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD, USA
    Int J Immunogenet 35:255-64. 2008
    ..01-0.04). These results suggest that IL10 and IL20 gene variants influence HBV infection outcome and encourage the pursuit of further studies of these cytokines in HBV pathogenesis...
  34. ncbi Genomics. A dog's breakfast?
    STEPHEN J O'BRIEN
    Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702, USA
    Science 301:1854-5. 2003
    ..As they explain, even though the coverage of the dog genome (1.5x) is lower than that of mouse (8x), there are many valuable insights to be gained from comparing the sequence of dog with those of mouse and human...
  35. ncbi The effect of RANTES chemokine genetic variants on early HIV-1 plasma RNA among African American injection drug users
    Priya Duggal
    Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
    J Acquir Immune Defic Syndr 38:584-9. 2005
    ..Because RANTES is a critical chemokine and competitively inhibits HIV-1 by binding to its receptor CCR5, treatment to enhance RANTES expression may assist in delaying the progression of AIDS by decreasing the initial viral load...
  36. ncbi Behavioral risk exposure and host genetics of susceptibility to HIV-1 infection
    Sadeep Shrestha
    Laboratory of Genomic Diversity, National Cancer Institute at Frederick, National Institutes of Health, MD 21702, USA
    J Infect Dis 193:16-26. 2006
    ..The matched case-control study design with measured risk exposures provides an avenue for discovering genes involved in susceptibility to infection...
  37. ncbi A molecular phylogeny for bats illuminates biogeography and the fossil record
    Emma C Teeling
    Laboratory of Genomic Diversity, Basic Research Program, SAIC Frederick, Inc, National Cancer Institute, Frederick, MD 21702, USA
    Science 307:580-4. 2005
    ....
  38. ncbi Development of Y chromosome intraspecific polymorphic markers in the Felidae
    Shu Jin Luo
    Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702 1201, USA
    J Hered 98:400-13. 2007
    ....
  39. ncbi Genomics. Mmu 16--comparative genomic highlights
    Neal G Copeland
    Mouse Cancer Genetics Program, National Cancer Institute, Frederick, MD, 21702, USA
    Science 296:1617-8. 2002
  40. pmc KIR/HLA pleiotropism: protection against both HIV and opportunistic infections
    Ying Qi
    Laboratory of Genomic Diversity, SAIC Frederick, Inc, National Cancer Institute, Frederick, Maryland, USA
    PLoS Pathog 2:e79. 2006
    ..The double protection of KIR3DS1/Bw4-80I in an etiologically complex disease such as AIDS, along with the disease specificity of its effects is conceptually novel and underscores the intricacy of host immunogenetics against HIV/AIDS...
  41. pmc Consistent effects of TSG101 genetic variability on multiple outcomes of exposure to human immunodeficiency virus type 1
    Arman A Bashirova
    Laboratory of Genomic Diversity, SAIC Frederick, Inc, National Cancer Institute, Frederick, Maryland 21702, USA
    J Virol 80:6757-63. 2006
    ..The data raise the hypothesis that noncoding variation in TSG101 affects the efficiency of TSG101-mediated release of viral particles from infected cells, thereby altering levels of plasma viral load and subsequent disease progression...
  42. pmc A domestic cat X chromosome linkage map and the sex-linked orange locus: mapping of orange, multiple origins and epistasis over nonagouti
    Anne Schmidt-Küntzel
    Laboratory of Genomic Diversity, Science Applications International Corporation, Frederick, MD 21702, USA
    Genetics 181:1415-25. 2009
    ..5 Mb and suggested multiple origins for the orange phenotype in the domestic cat. Furthermore, epistasis of orange over nonagouti was demonstrated at the genetic level...
  43. pmc An autosomal genetic linkage map of the domestic cat, Felis silvestris catus
    Marilyn Menotti-Raymond
    Laboratory of Genomic Diversity, National Cancer Institute Frederick, Frederick, MD 21702, USA
    Genomics 93:305-13. 2009
    ..The improved linkage map will provide an added resource for the mapping of phenotypic variation in the domestic cat and the use of this species as a model system for biological research...
  44. pmc Regulatory polymorphisms in the cyclophilin A gene, PPIA, accelerate progression to AIDS
    Ping An
    Laboratory of Genomic Diversity, Science Applications International Corporation Frederick, National Cancer Institute Frederick, Frederick, Maryland, United States of America
    PLoS Pathog 3:e88. 2007
    ..These results implicate regulatory PPIA polymorphisms as a component of genetic susceptibility to HIV-1 infection or disease progression, affirming the important role of PPIA in HIV-1 pathogenesis...
  45. pmc The evolutionary dynamics of the lion Panthera leo revealed by host and viral population genomics
    Agostinho Antunes
    Laboratory of Genomic Diversity, National Cancer Institute, Frederick, Maryland, United States of America
    PLoS Genet 4:e1000251. 2008
    ..In particular, lion and FIV(Ple) variation affirms that the large, well-studied lion population occupying the greater Serengeti Ecosystem is derived from three distinct populations that admixed recently...
  46. ncbi A homozygous single-base deletion in MLPH causes the dilute coat color phenotype in the domestic cat
    Yasuko Ishida
    Laboratory of Genomic Diversity, National Cancer Institute, Building 560, Room 11 38, Fort Detrick, Frederick, MD 21702, USA
    Genomics 88:698-705. 2006
    ..00001). Single-nucleotide polymorphism analyses in dilute individuals identified a single haplotype in dilute cats, suggesting that a single mutation event in MLPH gave rise to dilute in domestic cats...
  47. pmc Pathological manifestations of feline immunodeficiency virus (FIV) infection in wild African lions
    Melody E Roelke
    Laboratory of Genomic Diversity, SAIC Frederick, Inc, NCI Frederick, Frederick, MD, USA
    Virology 390:1-12. 2009
    ....
  48. pmc Examination of disease-based selection, demographic history and population structure in European Y-chromosome haplogroup I
    Efe Sezgin
    Laboratory of Genomic Diversity, National Cancer Institute at Frederick, Frederick, MD 21702 1201, USA
    J Hum Genet 55:613-20. 2010
    ..Clearly, further studies on Y-chromosome candidate loci sequencing to discover functional variants and discern the roles of evolutionary factors are warranted...
  49. ncbi AIDS restriction HLA allotypes target distinct intervals of HIV-1 pathogenesis
    Xiaojiang Gao
    Laboratory of Genomic Diversity, NCI Frederick, Basic Research Program, SAIC Frederick, P O Box B, Frederick, Maryland 21702, USA
    Nat Med 11:1290-2. 2005
    ..The discrete timing of HLA allele influence suggests alternative functional mechanisms in immune defense against this dynamic and chronic immunosuppressive disease...
  50. pmc Evolutionary analysis of a large mtDNA translocation (numt) into the nuclear genome of the Panthera genus species
    Jae Heup Kim
    Laboratory of Genomic Diversity, National Cancer Institute Frederick Cancer Research and Development Center NCI FCRDC, Frederick, MD 21702 1201, USA
    Gene 366:292-302. 2006
    ..The tiger cymtDNA shared around 90% sequence identity with the homologous numt sequence, suggesting an origin for the Panthera numt at around 3.5 million years ago, prior to the radiation of the five extant Panthera species...
  51. ncbi A tumor necrosis factor-alpha-inducible promoter variant of interferon-gamma accelerates CD4+ T cell depletion in human immunodeficiency virus-1-infected individuals
    Ping An
    Basic Research Program, SAIC Frederick, Inc, National Cancer Institute, Frederick, MD 21702, USA
    J Infect Dis 188:228-31. 2003
    ..It is possible that increased IFN-gamma production induced by TNF-alpha when -179T is present causes CD4 cell depletion by apoptosis...
  52. pmc Four independent mutations in the feline fibroblast growth factor 5 gene determine the long-haired phenotype in domestic cats
    JAMES S KEHLER
    The Laboratory of Genomic Diversity, National Cancer Institute Frederick, Frederick, MD 21702, USA
    J Hered 98:555-66. 2007
    ..In combination, these genomic approaches demonstrated that FGF5 is the major genetic determinant of hair length in the domestic cat...
  53. pmc Reconstructing the genomic architecture of mammalian ancestors using multispecies comparative maps
    William J Murphy
    Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702, USA
    Hum Genomics 1:30-40. 2003
    ....
  54. ncbi Dominant effects of CCR2-CCR5 haplotypes in HIV-1 disease progression
    Cheryl A Winkler
    Laboratory of Genomic Diversity, Division of Basic Research, SAIC Frederick, NCI, Frederick, MD, USA
    J Acquir Immune Defic Syndr 37:1534-8. 2004
    ....
  55. ncbi A mutation in KIR3DS1 that results in truncation and lack of cell surface expression
    Maureen P Martin
    Laboratory of Genomic Diversity, SAIC Frederick, Inc, NCI Frederick, Frederick, MD 21702, USA
    Immunogenetics 59:823-9. 2007
    ..The data indicate that the null KIR3DS1 allele is uncommon, arose on a single haplotype, and spread across geographically distinct populations...
  56. pmc Genomic microsatellites as evolutionary chronometers: a test in wild cats
    Carlos A Driscoll
    Intramural Research Support Program, SAIC Frederick, National Cancer Institute Frederick, Frederick, MD 21702 1201, USA
    Genome Res 12:414-23. 2002
    ....
  57. pmc FIV cross-species transmission: an evolutionary prospective
    Jennifer L Troyer
    Laboratory of Genomic Diversity, SAIC Frederick, Inc, NCI Frederick, Frederick, MD 21702, United States
    Vet Immunol Immunopathol 123:159-66. 2008
    ..These studies illustrate the utility of FIV as a model to discover the variables necessary for establishment and control of lentiviral infections in new species...
  58. ncbi HLA-B Bw4 alleles and HIV-1 transmission in heterosexual couples
    Tania M Welzel
    Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD 20892, USA
    AIDS 21:225-9. 2007
    ..Genetic factors may play a role in the transmission of HIV-1. Because HLA-B alleles influence HIV-1 disease progression and viral levels, they might also influence HIV-1 transmission...
  59. pmc Evolution of feline immunodeficiency virus in Felidae: implications for human health and wildlife ecology
    Jill Pecon-Slattery
    Laboratory of Genomic Diversity, National Cancer Institute Frederick, Frederick, MD 21702, United States
    Vet Immunol Immunopathol 123:32-44. 2008
    ....
  60. pmc Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression
    Sher L Hendrickson
    Laboratory of Genomic Diversity, National Cancer Institute, Frederick, Maryland, USA
    PLoS ONE 5:e12862. 2010
    ..Mitochondrial pathogenesis occurs in HIV patients and genetically, mitochondrial DNA haplogroups with presumed functional differences have been associated with differential AIDS progression...
  61. ncbi The Near Eastern origin of cat domestication
    Carlos A Driscoll
    Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702, USA
    Science 317:519-23. 2007
    ..Domestic cats derive from at least five founders from across this region, whose descendants were transported across the world by human assistance...
  62. pmc Genomically intact endogenous feline leukemia viruses of recent origin
    Alfred L Roca
    Laboratory of Genomic Diversity, Basic Research Program, SAIC Frederick, Maryland 21702, USA
    J Virol 78:4370-5. 2004
    ....
  63. pmc Patterns of feline immunodeficiency virus multiple infection and genome divergence in a free-ranging population of African lions
    Jennifer L Troyer
    Laboratory of Genomic Diversity, National Cancer Institute Frederick IRSP Program, SAIC Frederick, Frederick, Maryland 21702, USA
    J Virol 78:3777-91. 2004
    ..This comprehensive study of FIV-Ple in a free-ranging population of lions reveals a dynamic transmission of virus in a social species that has historically adapted to render the virus benign...
  64. pmc Role of exonic variation in chemokine receptor genes on AIDS: CCRL2 F167Y association with pneumocystis pneumonia
    Ping An
    Basic Research Laboratory, SAIC Frederick, National Cancer Institute Frederick, Frederick, Maryland, USA
    PLoS Genet 7:e1002328. 2011
    ..28-6.31) among four major AIDS-defining conditions. Considering the newly defined role of CCRL2 in lung dendritic cell trafficking, this atypical chemokine receptor may affect PCP through immune regulation and inducing inflammation...
  65. pmc Genetic protection against hepatitis B virus conferred by CCR5Delta32: Evidence that CCR5 contributes to viral persistence
    Chloe L Thio
    Department of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
    J Virol 81:441-5. 2007
    ....
  66. pmc Genome-wide association study implicates PARD3B-based AIDS restriction
    Jennifer L Troyer
    Laboratory of Genomic Diversity, SAIC Frederick, Inc, Frederick, MD 21702, USA
    J Infect Dis 203:1491-502. 2011
    ..Here we used clinically well-characterized subjects from 5 pretreatment HIV/AIDS cohorts for a genome-wide association study to identify gene associations with rate of AIDS progression...
  67. ncbi Comparative genomic structure of human, dog, and cat MHC: HLA, DLA, and FLA
    Naoya Yuhki
    Laboratory of Genomic Diversity, National Cancer Institute at Frederick, Frederick, MD 21702 1201, USA
    J Hered 98:390-9. 2007
    ....
  68. pmc Genetic associations of variants in genes encoding HIV-dependency factors required for HIV-1 infection
    Leslie W Chinn
    National Cancer Institute, Rockville, MD, USA
    J Infect Dis 202:1836-45. 2010
    ..Genes conferring a significant effect were termed HIV-dependency factors (HDFs)...
  69. ncbi Mitochondrial haplogroups are associated with risk of neuroretinal disorder in HIV-positive patients
    Sher L Hendrickson
    Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702 1201, USA
    J Acquir Immune Defic Syndr 53:451-5. 2010
    ..5% vs. 8.9% in patients with vs. without haplogroup J, respectively, P = 0.05). These data suggest that mitochondrial genotype may influence propensity to develop HIV-associated NRD in patients with AIDS...
  70. pmc Sequences, annotation and single nucleotide polymorphism of the major histocompatibility complex in the domestic cat
    Naoya Yuhki
    Laboratory of Genomic Diversity, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
    PLoS ONE 3:e2674. 2008
    ..84 Mbp (0.00411 SNP per bp), which is 2.4 times higher rate than average heterozygous region in the WGS (0.0017 SNP per bp genome), and slightly higher than the SNP rate observed in human MHC (0.00337 SNP per bp)...
  71. ncbi Diversity of MICA and linkage disequilibrium with HLA-B in two North American populations
    Xiaojiang Gao
    Laboratory of Genomic Diversity, NCI Frederick, Basic Research Program, SAIC Frederick, Frederick, MD 21702, USA
    Hum Immunol 67:152-8. 2006
    ..The lack of evidence for an active diversification of the MICA gene after racial separation indicates an evolutionary history distinct from that of the classical HLA genes...
  72. ncbi Mitochondrial introgressions into the nuclear genome of the domestic cat
    Agostinho Antunes
    Laboratory of Genomic Diversity, National Cancer Institute Frederick Cancer Research and Development Center, Frederick, MD 21702 1201, USA
    J Hered 98:414-20. 2007
    ..The catalog of cat numts provides a valuable resource for future studies in Felidae species, including its use as a tool to avoid numt contaminations that may confound population genetics and phylogenetic studies...
  73. pmc APOBEC3G genetic variants and their influence on the progression to AIDS
    Ping An
    Basic Research Program, SAIC Frederick, National Cancer Institute Frederick Cancer Research and Development Center, Frederick, MD 21702, USA
    J Virol 78:11070-6. 2004
    ..These studies suggest that there may be a modifying role of variants of APOBEC3G on HIV-1 disease progression that warrants further investigation...
  74. ncbi A population genetic database of cat breeds developed in coordination with a domestic cat STR multiplex
    Marilyn Menotti-Raymond
    Laboratory of Genomic Diversity, National Cancer Institute Frederick, Building 560, Room 11 38, Frederick, MD 21702, USA
    J Forensic Sci 57:596-601. 2012
    ..Heterozygosities obtained for the 10 loci range from 0.72 to 0.96. The power for genetic individualization of domestic cat samples of the multiplex is high, with a probability of match (p(m)) of 6.2E-14, using a conservative θ = 0.05...
  75. pmc Genetics and pathogenesis of feline infectious peritonitis virus
    Meredith A Brown
    Laboratory of Genomic Diversity, National Cancer Institute, Frederick, Maryland 21702, USA
    Emerg Infect Dis 15:1445-52. 2009
    ..In addition, 5 membrane protein amino acid residues with functional potential differentiated healthy cats from cats with FIP. These findings may have potential as diagnostic markers for virulent FIP-associated FCoV...
  76. ncbi Haplotype diversity in the interleukin-4 gene is not associated with HIV-1 transmission and AIDS progression
    William S Modi
    Basic Research Program, SAIC Frederick, National Cancer Institute FCRDC, Frederick, MD 21702 1201, USA
    Immunogenetics 55:157-64. 2003
    ..Present analyses failed to identify any significant associations with HIV-1 infection or progression to AIDS...
  77. ncbi Subspecies genetic assignments of worldwide captive tigers increase conservation value of captive populations
    Shu Jin Luo
    Laboratory of Genomic Diversity, National Cancer Institute, Frederick, Maryland 21702, USA
    Curr Biol 18:592-6. 2008
    ..Assessment of verified subspecies ancestry offers a powerful tool that, if applied to tigers of uncertain background, may considerably increase the number of purebred tigers suitable for conservation management...
  78. pmc Effect of host genetics on the development of cytomegalovirus retinitis in patients with AIDS
    Efe Sezgin
    Laboratory of Genomic Diversity, SAIC Frederick, National Cancer Institute, Frederick, Maryland 21702 1201, USA
    J Infect Dis 202:606-13. 2010
    ..The ubiquitous CMV pathogen contains a human interleukin-10 (IL-10) homolog in its genome and utilizes it to evade host immune reactions through an IL-10 receptor mediated immune-suppression pathway...
  79. pmc FIV diversity: FIV Ple subtype composition may influence disease outcome in African lions
    Jennifer L Troyer
    Laboratory of Genomic Diversity, SAIC Frederick, National Cancer Institute, Frederick, MD, USA
    Vet Immunol Immunopathol 143:338-46. 2011
    ....
  80. pmc Initial sequence and comparative analysis of the cat genome
    Joan U Pontius
    Laboratory of Genomic Diversity, SAIC Frederick, Inc, NCI Frederick, Frederick, Maryland 21702, USA
    Genome Res 17:1675-89. 2007
    ..9-fold) coverage mammal genome sequence...
  81. pmc Association of DC-SIGN promoter polymorphism with increased risk for parenteral, but not mucosal, acquisition of human immunodeficiency virus type 1 infection
    Maureen P Martin
    Basic Research Program, SAIC Frederick, National Cancer Institute, MD 21702, USA
    J Virol 78:14053-6. 2004
    ..87, P = 0.001). This association was not observed in those at risk for mucosally acquired infection. A potential role for DC-SIGN specific to systemic acquisition and dissemination of infection is suggested...
  82. pmc Identifying selected regions from heterozygosity and divergence using a light-coverage genomic dataset from two human populations
    Taras K Oleksyk
    Laboratory of Genomic Diversity, National Cancer Institute at Frederick, Frederick, Maryland, USA
    PLoS ONE 3:e1712. 2008
    ..The main strength of our analysis method compared to others is that it does not require dense genotyping and therefore can be used with data from population-based genome SNP scans from smaller studies of humans or other species...
  83. pmc Mutation discovered in a feline model of human congenital retinal blinding disease
    Marilyn Menotti-Raymond
    Laboratory of Genomic Diversity, National Cancer Institute Frederick, Frederick, Maryland 21702, USA
    Invest Ophthalmol Vis Sci 51:2852-9. 2010
    ..Disease expression in Rdy cats is comparable to that in young patients with congenital blindness (Leber congenital amaurosis [LCA] or retinitis pigmentosa [RP])...
  84. ncbi Gene conversion between mammalian CCR2 and CCR5 chemokine receptor genes: a potential mechanism for receptor dimerization
    Nuria Vazquez-Salat
    Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702, USA
    Genomics 90:213-24. 2007
    ....
  85. pmc Mapping of the domestic cat "SILVER" coat color locus identifies a unique genomic location for silver in mammals
    Marilyn Menotti-Raymond
    Laboratory of Genomic Diversity, National Cancer Institute Frederick, Frederick, MD 21702, USA
    J Hered 100:S8-13. 2009
    ....
  86. ncbi Mammalian phylogenomics comes of age
    William J Murphy
    Basic Research Laboratory, SAIC Frederick, Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702, USA
    Trends Genet 20:631-9. 2004
    ....
  87. pmc Insertional polymorphisms of endogenous feline leukemia viruses
    Alfred L Roca
    Laboratory of Genomic Diversity, Basic Research Program, SAIC Frederick, Maryland, USA
    J Virol 79:3979-86. 2005
    ..Since endogenous FeLVs may affect the infectiousness or pathogenicity of exogenous FeLVs, genomic variation in enFeLVs represents a candidate for genetic influences on FeLV leukemogenesis in cats...
  88. ncbi Epistatic interaction between KIR3DS1 and HLA-B delays the progression to AIDS
    Maureen P Martin
    Basic Research Program, SAIC Frederick, Frederick, Maryland 21702 1201, USA
    Nat Genet 31:429-34. 2002
    ..The strongest synergistic effect of these loci was on progression to depletion of CD4(+) T cells, which suggests that a protective response of NK cells involving KIR3DS1 and its HLA class I ligands begins soon after HIV-1 infection...
  89. pmc Mitochondrial DNA haplogroups influence lipoatrophy after highly active antiretroviral therapy
    Sher L Hendrickson
    Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702 1201
    J Acquir Immune Defic Syndr 51:111-6. 2009
    ..05, OR = 0.52, 95% CI = 0.20 to 1.00). These data suggest that mitochondrial DNA haplogroup may influence the propensity for lipoatrophy in patients receiving nucleoside reverse transcriptase inhibitors...
  90. ncbi Molecular evidence for species-level distinctions in clouded leopards
    Valerie A Buckley-Beason
    Laboratory of Genomic Diversity, National Cancer Institute, Frederick, Maryland 21702, USA
    Curr Biol 16:2371-6. 2006
    ..n. diardi in Borneo and Sumatra, would support reclassification of N. n. diardi as a new species (Neofelis diardi)...
  91. doi Genetic restoration of the Florida panther
    Warren E Johnson
    Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702, USA
    Science 329:1641-5. 2010
    ..This intensive management program illustrates the challenges of maintaining populations of large predators worldwide...
  92. doi Evaluation of nonviral risk factors for nasopharyngeal carcinoma in a high-risk population of Southern China
    Xiuchan Guo
    Laboratory of Genomic Diversity, SAIC Frederick, Inc, NCI Frederick, Frederick, MD 21702, USA
    Int J Cancer 124:2942-7. 2009
    ..7% of NPC development in NPC high risk population. These findings should have important public health implications for NPC risk reduction in endemic regions...
  93. ncbi Life on the edge: the long-term persistence and contrasting spatial genetic structure of distinct brown trout life histories at their ecological limits
    Agostinho Antunes
    CIBIO UP, Centro de Investigacao em Biodiversidade e Recursos Geneticos, Campus Agrário de Vairão, 4485 661 Vairão, Portugal
    J Hered 97:193-205. 2006
    ..These peripheral populations are of high conservation value and should be preserved to help conserve the future potential of the species...
  94. ncbi Molecular genetics and evolution of melanism in the cat family
    Eduardo Eizirik
    Laboratory of Genomic Diversity, NCI Frederick, National Institutes of Health, Frederick, MD 21702 1201, USA
    Curr Biol 13:448-53. 2003
    ..The inferred multiple origins and independent historical elevation in population frequency of felid melanistic mutations suggest the occurrence of adaptive evolution of this visible phenotype in a group of related free-ranging species...
  95. ncbi Patterns of molecular genetic variation among cat breeds
    Marilyn Menotti-Raymond
    Laboratory of Genomic Diversity, National Cancer Institute Frederick, Frederick, MD 21702, USA
    Genomics 91:1-11. 2008
    ....
  96. pmc Artifacts of the 1.9x feline genome assembly derived from the feline-specific satellite sequence
    Joan U Pontius
    Laboratory of Genomic Diversity, Basic Research Program, Science Applications International Corporation Frederick, Inc, National Cancer Institute Frederick, Frederick, MD 21702, USA
    J Hered 100:S14-8. 2009
    ..The findings regarding the feline-specific sequence should be considered in the pending 8x assembly of the cat genome...
  97. pmc Feline immunodeficiency virus (FIV) in wild Pallas' cats
    Meredith A Brown
    Laboratory of Genomic Diversity, National Cancer Institute Frederick, Frederick, MD 21702, USA
    Vet Immunol Immunopathol 134:90-5. 2010
    ..Histopathological examination of lymph node and spleen from infected and uninfected Pallas' cats suggests that FIV(Oma) causes immune depletion in its' native host...
  98. pmc A common HLA-DPA1 variant is a major determinant of hepatitis B virus clearance in Han Chinese
    Ping An
    Basic Research Laboratory, SAIC Frederick, Maryland, USA
    J Infect Dis 203:943-7. 2011
    ..We showed for the first time to our knowledge that it is a predictor for HBV clearance (odds ratio, 2.41; P < .001). However, rs3077 was not associated with the development of cirrhosis or hepatocellular carcinoma...
  99. pmc A molecular phylogeny of living primates
    Polina Perelman
    Laboratory of Genomic Diversity, National Cancer Institute Frederick, Frederick, Maryland, USA
    PLoS Genet 7:e1001342. 2011
    ....