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• {"link"=>{"url"=>"http://www.citeulike.org/user/songpku/article/6389592"}, "post_time"=>"2009-12-16 20:19:52", "tag"=>["cytokine", "immune", "inflammation", "nfkb", "nhl", "polymorphism", "snp", "susceptibility", "tnf"], "linkout"=>[{"type"=>"DOI", "url"=>"http://dx.doi.org/10.1371/journal.pone.0005360"}, {"type"=>"Pubmed", "url"=>"http://view.ncbi.nlm.nih.gov/pubmed/19390683"}, {"type"=>"Hubmed", "url"=>"http://www.hubmed.org/display.cgi?uids=19390683"}], "username"=>"songpku", "article_id"=>"6389592"}

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{"title"=>"Common gene variants in the Tumor Necrosis Factor (TNF) and TNF receptor superfamilies and NF-kB transcription factors and non-hodgkin lymphoma risk", "type"=>"journal", "authors"=>[{"first_name"=>"Sophia S.", "last_name"=>"Wang", "scopus_author_id"=>"37085752800"}, {"first_name"=>"Mark P.", "last_name"=>"Purdue", "scopus_author_id"=>"6701653966"}, {"first_name"=>"James R.", "last_name"=>"Cerhan", "scopus_author_id"=>"7005949363"}, {"first_name"=>"Tongzhang", "last_name"=>"Zheng", "scopus_author_id"=>"7201358801"}, {"first_name"=>"Idan", "last_name"=>"Menashe", "scopus_author_id"=>"24328403000"}, {"first_name"=>"Bruce K.", "last_name"=>"Armstrong", "scopus_author_id"=>"55454358900"}, {"first_name"=>"Qing", "last_name"=>"Lan", "scopus_author_id"=>"56682598900"}, {"first_name"=>"Patricia", "last_name"=>"Hartge", "scopus_author_id"=>"7005897469"}, {"first_name"=>"Anne", "last_name"=>"Kricker", "scopus_author_id"=>"7005723030"}, {"first_name"=>"Yawei", "last_name"=>"Zhang", "scopus_author_id"=>"7601312676"}, {"first_name"=>"Lindsay M.", "last_name"=>"Morton", "scopus_author_id"=>"7006491443"}, {"first_name"=>"Claire M.", "last_name"=>"Vajdic", "scopus_author_id"=>"6603573607"}, {"first_name"=>"Theodore R.", "last_name"=>"Holford", "scopus_author_id"=>"7007135966"}, {"first_name"=>"Richard K.", "last_name"=>"Severson", "scopus_author_id"=>"7005585553"}, {"first_name"=>"Andrew", "last_name"=>"Grulich", "scopus_author_id"=>"7005960643"}, {"first_name"=>"Brian P.", "last_name"=>"Leaderer", "scopus_author_id"=>"7006785806"}, {"first_name"=>"Scott", "last_name"=>"Davis", "scopus_author_id"=>"55465579200"}, {"first_name"=>"Wendy", "last_name"=>"Cozen", "scopus_author_id"=>"6603803363"}, {"first_name"=>"Meredith", "last_name"=>"Yeager", "scopus_author_id"=>"35379327500"}, {"first_name"=>"Stephen J.", "last_name"=>"Chanock", "scopus_author_id"=>"7006047196"}, {"first_name"=>"Nilanjan", "last_name"=>"Chatterjee", "scopus_author_id"=>"7102740943"}, {"first_name"=>"Nathaniel", "last_name"=>"Rothman", "scopus_author_id"=>"7005049561"}], "year"=>2009, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "pui"=>"354546710", "doi"=>"10.1371/journal.pone.0005360", "sgr"=>"65449169623", "scopus"=>"2-s2.0-65449169623", "isbn"=>"1932-6203 (Electronic)", "pmid"=>"19390683"}, "id"=>"4ec11df4-c205-3b0a-a2d4-120ac37d03f2", "abstract"=>"BACKGROUND: A promoter polymorphism in the pro-inflammatory cytokine tumor necrosis factor (TNF) (TNF G-308A) is associated with increased non-Hodgkin lymphoma (NHL) risk. The protein product, TNF-alpha, activates the nuclear factor kappa beta (NF-kappaB) transcription factor, and is critical for inflammatory and apoptotic responses in cancer progression. We hypothesized that the TNF and NF-kappaB pathways are important for NHL and that gene variations across the pathways may alter NHL risk. METHODOLOGY/PRINCIPAL FINDINGS: We genotyped 500 tag single nucleotide polymorphisms (SNPs) from 48 candidate gene regions (defined as 20 kb 5', 10 kb 3') in the TNF and TNF receptor superfamilies and the NF-kappaB and related transcription factors, in 1946 NHL cases and 1808 controls pooled from three independent population-based case-control studies. We obtained a gene region-level summary of association by computing the minimum p-value (\"minP test\"). We used logistic regression to compute odds ratios and 95% confidence intervals for NHL and four major NHL subtypes in relation to SNP genotypes and haplotypes. For NHL, the tail strength statistic supported an overall relationship between the TNF/NF-kappaB pathway and NHL (p = 0.02). We confirmed the association between TNF/LTA on chromosome 6p21.3 with NHL and found the LTA rs2844484 SNP most significantly and specifically associated with the major subtype, diffuse large B-cell lymphoma (DLBCL) (p-trend = 0.001). We also implicated for the first time, variants in NFKBIL1 on chromosome 6p21.3, associated with NHL. Other gene regions identified as statistically significantly associated with NHL included FAS, IRF4, TNFSF13B, TANK, TNFSF7 and TNFRSF13C. Accordingly, the single most significant SNPs associated with NHL were FAS rs4934436 (p-trend = 0.0024), IRF4 rs12211228 (p-trend = 0.0026), TNFSF13B rs2582869 (p-trend = 0.0055), TANK rs1921310 (p-trend = 0.0025), TNFSF7 rs16994592 (p-trend = 0.0024), and TNFRSF13C rs6002551 (p-trend = 0.0074). All associations were consistent in each study with no apparent specificity for NHL subtype. CONCLUSIONS/SIGNIFICANCE: Our results provide consistent evidence that variation in the TNF superfamily of genes and specifically within chromosome 6p21.3 impacts lymphomagenesis. Further characterization of these susceptibility loci and identification of functional variants are warranted.", "link"=>"http://www.mendeley.com/research/common-gene-variants-tumor-necrosis-factor-tnf-tnf-receptor-superfamilies-nfkb-transcription-factors", "reader_count"=>38, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Student > Doctoral Student"=>4, "Researcher"=>12, "Student > Ph. D. Student"=>10, "Student > Master"=>5, "Other"=>1, "Student > Bachelor"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Student > Doctoral Student"=>4, "Researcher"=>12, "Student > Ph. D. Student"=>10, "Student > Master"=>5, "Other"=>1, "Student > Bachelor"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Biochemistry, Genetics and Molecular Biology"=>5, "Medicine and Dentistry"=>18, "Agricultural and Biological Sciences"=>11, "Chemistry"=>1, "Social Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>18}, "Chemistry"=>{"Chemistry"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>11}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}, "Unspecified"=>{"Unspecified"=>2}}, "reader_count_by_country"=>{"Canada"=>1, "United States"=>2}, "group_count"=>1}

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Figshare

• {"files"=>["https://ndownloader.figshare.com/files/445569", "https://ndownloader.figshare.com/files/445667", "https://ndownloader.figshare.com/files/445811", "https://ndownloader.figshare.com/files/445849", "https://ndownloader.figshare.com/files/445879", "https://ndownloader.figshare.com/files/445902", "https://ndownloader.figshare.com/files/445932", "https://ndownloader.figshare.com/files/445961"], "description"=>"<div><h3>Background</h3><p>A promoter polymorphism in the pro-inflammatory cytokine tumor necrosis factor (<em>TNF</em>) (<em>TNF</em> G-308A) is associated with increased non-Hodgkin lymphoma (NHL) risk. The protein product, TNF-α, activates the nuclear factor kappa beta (NF-κB) transcription factor, and is critical for inflammatory and apoptotic responses in cancer progression. We hypothesized that the TNF and NF-κB pathways are important for NHL and that gene variations across the pathways may alter NHL risk.</p><h3>Methodology/Principal Findings</h3><p>We genotyped 500 tag single nucleotide polymorphisms (SNPs) from 48 candidate gene regions (defined as 20 kb 5′, 10 kb 3′) in the TNF and TNF receptor superfamilies and the NF-κB and related transcription factors, in 1946 NHL cases and 1808 controls pooled from three independent population-based case-control studies. We obtaineded a gene region-level summary of association by computing the minimum p-value (“minP test”). We used logistic regression to compute odds ratios and 95% confidence intervals for NHL and four major NHL subtypes in relation to SNP genotypes and haplotypes. For NHL, the tail strength statistic supported an overall relationship between the TNF/NF-κB pathway and NHL (p = 0.02). We confirmed the association between <em>TNF</em>/<em>LTA</em> on chromosome 6p21.3 with NHL and found the <em>LTA</em> rs2844484 SNP most significantly and specifically associated with the major subtype, diffuse large B-cell lymphoma (DLBCL) (p-trend = 0.001). We also implicated for the first time, variants in <em>NFKBIL1</em> on chromosome 6p21.3, associated with NHL. Other gene regions identified as statistically significantly associated with NHL included <em>FAS</em>, <em>IRF4</em>, <em>TNFSF13B</em>, <em>TANK</em>, <em>TNFSF7</em> and <em>TNFRSF13C</em>. Accordingly, the single most significant SNPs associated with NHL were <em>FAS</em> rs4934436 (p-trend = 0.0024), <em>IRF4</em> rs12211228 (p-trend = 0.0026), <em>TNFSF13B</em> rs2582869 (p-trend = 0.0055), <em>TANK</em> rs1921310 (p-trend = 0.0025), <em>TNFSF7</em> rs16994592 (p-trend = 0.0024), and <em>TNFRSF13C</em> rs6002551 (p-trend = 0.0074). All associations were consistent in each study with no apparent specificity for NHL subtype.</p><h3>Conclusions/Significance</h3><p>Our results provide consistent evidence that variation in the TNF superfamily of genes and specifically within chromosome 6p21.3 impacts lymphomagenesis. Further characterization of these susceptibility loci and identification of functional variants are warranted.</p></div>", "links"=>[], "tags"=>["variants", "necrosis", "tnf", "receptor", "superfamilies", "nf-kb", "transcription", "factors", "non-hodgkin", "lymphoma"], "article_id"=>147816, "categories"=>["Genetics", "Biotechnology", "Hematology"], "users"=>["Sophia S. Wang", "Mark P. Purdue", "James R. Cerhan", "Tongzhang Zheng", "Idan Menashe", "Bruce K. Armstrong", "Qing Lan", "Patricia Hartge", "Anne Kricker", "Yawei Zhang", "Lindsay M. Morton", "Claire M. Vajdic", "Theodore R. Holford", "Richard K. Severson", "Andrew Grulich", "Brian P. Leaderer", "Scott Davis", "Wendy Cozen", "Meredith Yeager", "Stephen J. Chanock", "Nilanjan Chatterjee", "Nathaniel Rothman"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0005360.s001", "https://dx.doi.org/10.1371/journal.pone.0005360.s002", "https://dx.doi.org/10.1371/journal.pone.0005360.s003", "https://dx.doi.org/10.1371/journal.pone.0005360.s004", "https://dx.doi.org/10.1371/journal.pone.0005360.s005", "https://dx.doi.org/10.1371/journal.pone.0005360.s006", "https://dx.doi.org/10.1371/journal.pone.0005360.s007", "https://dx.doi.org/10.1371/journal.pone.0005360.s008"], "stats"=>{"downloads"=>37, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Common_Gene_Variants_in_the_Tumor_Necrosis_Factor_TNF_and_TNF_Receptor_Superfamilies_and_NF_kB_Transcription_Factors_and_Non_Hodgkin_Lymphoma_Risk/147816", "title"=>"Common Gene Variants in the Tumor Necrosis Factor (TNF) and TNF Receptor Superfamilies and NF-kB Transcription Factors and Non-Hodgkin Lymphoma Risk", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2009-04-24 02:10:16"}
• {"files"=>["https://ndownloader.figshare.com/files/899539"], "description"=>"<p>Data for all SNPs (pooled and by study) are shown in Supplemental Materials (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005360#pone.0005360.s005\" target=\"_blank\">Table S5</a>).</p>", "links"=>[], "tags"=>["intervals", "additive", "snps", "nhl", "pooled", "shown"], "article_id"=>569960, "categories"=>["Genetics", "Biotechnology", "Hematology"], "users"=>["Sophia S. Wang", "Mark P. Purdue", "James R. Cerhan", "Tongzhang Zheng", "Idan Menashe", "Bruce K. Armstrong", "Qing Lan", "Patricia Hartge", "Anne Kricker", "Yawei Zhang", "Lindsay M. Morton", "Claire M. Vajdic", "Theodore R. Holford", "Richard K. Severson", "Andrew Grulich", "Brian P. Leaderer", "Scott Davis", "Wendy Cozen", "Meredith Yeager", "Stephen J. Chanock", "Nilanjan Chatterjee", "Nathaniel Rothman"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0005360.g001", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Odds_ratios_95_confidence_intervals_of_additive_model_for_SNPs_with_p_trends_lt_0_01_for_NHL_in_pooled_analyses_data_also_shown_by_study_adjusted_for_age_sex_race_and_study_site_when_applicable_/569960", "title"=>"Odds ratios, 95% confidence intervals of additive model for SNPs with p-trends<0.01 for NHL in pooled analyses; data also shown by study (adjusted for age, sex, race, and study site, when applicable).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-04-24 02:46:00"}
• {"files"=>["https://ndownloader.figshare.com/files/899823"], "description"=>"<p>Detailed annotation of genes and SNPs shown in Supplemental Materials (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005360#pone.0005360.s002\" target=\"_blank\">Tables S2</a> and <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005360#pone.0005360.s003\" target=\"_blank\">S3</a>).</p>*<p>Gene regions defined as 20 kb 5′ and 10 kb 3′ of target gene.</p>", "links"=>[], "tags"=>["regions", "genes", "nhl", "case-control"], "article_id"=>570249, "categories"=>["Genetics", "Biotechnology", "Hematology"], "users"=>["Sophia S. Wang", "Mark P. Purdue", "James R. Cerhan", "Tongzhang Zheng", "Idan Menashe", "Bruce K. Armstrong", "Qing Lan", "Patricia Hartge", "Anne Kricker", "Yawei Zhang", "Lindsay M. Morton", "Claire M. Vajdic", "Theodore R. Holford", "Richard K. Severson", "Andrew Grulich", "Brian P. Leaderer", "Scott Davis", "Wendy Cozen", "Meredith Yeager", "Stephen J. Chanock", "Nilanjan Chatterjee", "Nathaniel Rothman"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0005360.t001", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_families_and_regions_of_analyzed_candidate_genes_in_three_independent_NHL_case_control_studies_/570249", "title"=>"Gene families and regions of analyzed candidate genes in three independent NHL case-control studies.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-04-24 00:04:09"}
• {"files"=>["https://ndownloader.figshare.com/files/899766"], "description"=>"<p>Genes selected are those with permutation p<0.05; results for all genes shown in Supplemental Materials (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005360#pone.0005360.s004\" target=\"_blank\">Table S4</a>).</p>1<p>p-value from tail-strength test.</p>2<p>p value from minP test.</p>*<p>likelihood ratio test (LRT) p = 0.0079.</p>**<p>LRT p = 0.049.</p>", "links"=>[], "tags"=>["levels", "pathway", "calculated", "permutation", "permutations", "p-trend", "nhl", "subtypes", "marginal"], "article_id"=>570192, "categories"=>["Genetics", "Biotechnology", "Hematology"], "users"=>["Sophia S. Wang", "Mark P. Purdue", "James R. Cerhan", "Tongzhang Zheng", "Idan Menashe", "Bruce K. Armstrong", "Qing Lan", "Patricia Hartge", "Anne Kricker", "Yawei Zhang", "Lindsay M. Morton", "Claire M. Vajdic", "Theodore R. Holford", "Richard K. Severson", "Andrew Grulich", "Brian P. Leaderer", "Scott Davis", "Wendy Cozen", "Meredith Yeager", "Stephen J. Chanock", "Nilanjan Chatterjee", "Nathaniel Rothman"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0005360.t002", "stats"=>{"downloads"=>6, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Significance_levels_p_values_for_the_TNF_NFkB_pathway_and_for_each_target_region_calculated_from_the_permutation_test_based_on_10_000_permutations_and_the_minimum_p_trend_within_each_region_for_the_association_with_NHL_and_NHL_subtypes_DLBCL_follicular_m/570192", "title"=>"Significance levels (p values) for the TNF/NFkB pathway and for each target region calculated from the permutation test [based on 10,000 permutations and the minimum p-trend within each region], for the association with NHL and NHL subtypes (DLBCL, follicular, marginal zone, and CLL/SLL).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-04-24 00:03:12"}
• {"files"=>["https://ndownloader.figshare.com/files/899651"], "description"=>"<p>Data for all SNPs by NHL subtype are shown in Supplemental Materials (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005360#pone.0005360.s006\" target=\"_blank\">Table S6</a>).</p>", "links"=>[], "tags"=>["intervals", "additive", "snps", "nhl", "pooled", "shown", "subtypes", "marginal", "lymphomas"], "article_id"=>570081, "categories"=>["Genetics", "Biotechnology", "Hematology"], "users"=>["Sophia S. Wang", "Mark P. Purdue", "James R. Cerhan", "Tongzhang Zheng", "Idan Menashe", "Bruce K. Armstrong", "Qing Lan", "Patricia Hartge", "Anne Kricker", "Yawei Zhang", "Lindsay M. Morton", "Claire M. Vajdic", "Theodore R. Holford", "Richard K. Severson", "Andrew Grulich", "Brian P. Leaderer", "Scott Davis", "Wendy Cozen", "Meredith Yeager", "Stephen J. Chanock", "Nilanjan Chatterjee", "Nathaniel Rothman"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0005360.g002", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Odds_ratios_95_confidence_intervals_of_additive_model_for_SNPs_with_p_trends_lt_0_01_for_NHL_in_pooled_analyses_data_shown_by_NHL_subtypes_DLBCL_follicular_CLL_SLL_and_marginal_zone_lymphomas_in_pooled_population_adjusted_for_age_sex_race_and_study_site_/570081", "title"=>"Odds ratios, 95% confidence intervals of additive model for SNPs with p-trends<0.01 for NHL in pooled analyses; data shown by NHL subtypes DLBCL, follicular, CLL/SLL and marginal zone lymphomas in pooled population (adjusted for age, sex, race, and study site).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-04-24 00:01:21"}

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Relative Metric

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F1000Prime