Journal: PLoS ONE

Article Title: Factors Associated to Vaccination against Influenza among Elderly in a Large Brazilian Metropolis

doi: 10.1371/journal.pone.0123840

Figure Lengend Snippet: Multiple variables analysis: Poisson regression model for influenza vaccination among the elderly (n = 1,341). São Paulo, Brazil, 2010.

Article Snippet: At last, the use of health services were adjusted for themselves, socio-demographic, behavioral and self-reported health variables Data analysis was used the Stata 12.0 2011 software (Stata Corporation, College Station, TX, USA).

Techniques: Activity Assay

Journal: Nature genetics

Article Title: Genome-wide association meta-analyses combining multiple risk phenotypes provides insights into the genetic architecture of cutaneous melanoma susceptibility

doi: 10.1038/s41588-020-0611-8

Figure Lengend Snippet: −log 10 of two-sided P-values for SNPs derived from a fixed-effects inverse variance weighted meta-analysis of logistic regression GWAS (Y-axis) plotted against SNP chromosome positions for the total meta-analysis (36,760 melanoma cases and 375,188 controls; for full details of analysis and covariates included see the ). The y-axis is limited to −log 10 (1×10 −25 ) to truncate strong signals at loci such as MC1R and ASIP . The full plot is displayed in . To account for multiple testing, SNPs with a P-value less than 5×10 −8 are deemed significant.

Article Snippet: The total meta-analysis includes self-report cutaneous melanoma GWAS data from the UK Biobank and 23andMe.

Techniques: Derivative Assay

Journal: Nature genetics

Article Title: Genome-wide association meta-analyses combining multiple risk phenotypes provides insights into the genetic architecture of cutaneous melanoma susceptibility

doi: 10.1038/s41588-020-0611-8

Figure Lengend Snippet: Quantile-quantile plots of negative log 10 two sided P-value derived from a fixed-effects inverse-variance weighted meta-analysis of log(OR) effect-sizes derived from the logistic regression GWAS listed in . All confirmed and self-report cases are included, with a total sample size of 36,760 melanoma cases and 375,188 controls.

Article Snippet: The total meta-analysis includes self-report cutaneous melanoma GWAS data from the UK Biobank and 23andMe.

Techniques: Derivative Assay

Journal: Nature genetics

Article Title: Genome-wide association meta-analyses combining multiple risk phenotypes provides insights into the genetic architecture of cutaneous melanoma susceptibility

doi: 10.1038/s41588-020-0611-8

Figure Lengend Snippet: Negative log 10 two sided P-value derived from a fixed-effects inverse-variance weighted meta-analysis of log(OR) effect-sizes derived from the logistic regression GWAS (y-axis) are plotted by their chromosome position. The confirmed-only analysis included 30,134 cases with histopathologically confirmed CM, and 81,415 controls. The total CM meta-analysis includes all confirmed and self-report cases, with a total sample size of 36,760 CM cases and 375,188 controls. Multiple-testing corrected genome-wide significance threshold was P<5×10 −8 . We display in order the total CM meta-analysis without limiting the y-axis; the pathologically confirmed CM cases only meta-analysis with the y-axis limited to 1×10 −25 and without a limit to more clearly display loci other than MC1R.

Article Snippet: The total meta-analysis includes self-report cutaneous melanoma GWAS data from the UK Biobank and 23andMe.

Techniques: Derivative Assay, Genome Wide

Journal: Nature genetics

Article Title: Genome-wide association meta-analyses combining multiple risk phenotypes provides insights into the genetic architecture of cutaneous melanoma susceptibility

doi: 10.1038/s41588-020-0611-8

Figure Lengend Snippet: Loci previously identified in cutaneous melanoma susceptibility GWAS. CHR, BP: hg19 positional information. rsID : dbSNP142 rs number. Pub lications. We also summarize Supplementary Table 3 ; Gene prioritizes the functional target if known, followed by melanocyte or skin tissue TWAS data, or finally the closest protein coding gene; ‘Multiple’ indicates three or more genes. GWS : We indicate with yes (Y) or no (N) whether this locus is genome-wide significant (P < 5 × 10 −8 ) in the total meta-analysis. The effect allele ( EA ) and non-effect allele ( NEA ) are listed, as are the effect allele Freq uency in the HRC reference panel 107 ; total fixed-effects inverse-variance weighted meta-analysis of logistic regression two-sided P-value ( P meta ) and Odds Ratio ( OR ) are from an additive model and are reported per-allele with respect to the EA. Reported results are for the total meta-analysis (36,760 melanoma cases and 375,188 controls; for full details of analysis and covariates included see Online Methods ). We also indicate whether this locus is associated with other traits: Nevi : Pleiotropically associated with cutaneous melanoma and nevus count ( Online Methods ; Supplementary Table 9 ); Hair : Pleiotropically associated with cutaneous melanoma and hair color ( Online Methods ; Supplementary Table 10 ). Tanning response ( Tan ) and Telomere length ( Telo ) indicates the lead SNP is associated with these traits when corrected for multiple testing ( Online Methods , Supplementary Table 5 ).

Article Snippet: The total meta-analysis includes self-report cutaneous melanoma GWAS data from the UK Biobank and 23andMe.

Techniques: Functional Assay, Genome Wide, Significance Assay

Journal: Nature genetics

Article Title: Genome-wide association meta-analyses combining multiple risk phenotypes provides insights into the genetic architecture of cutaneous melanoma susceptibility

doi: 10.1038/s41588-020-0611-8

Figure Lengend Snippet: Novel loci not previously identified in cutaneous melanoma GWAS. CHR, BP: hg19 position. rsID : dbSNP142 rs number. Gene prioritizes the functional target if known, followed by melanocyte or skin tissue TWAS data, or finally the closest protein coding gene; multiple indicates three or more genes ( Supplementary Table 3 ). The effect allele ( EA ) and non-effect allele ( NEA ) are listed, as are the effect allele Freq uency in the HRC reference panel 107 ; total fixed-effects inverse-variance weighted meta-analysis of logistic regression two-sided P-values and Odds Ratio ( OR ) are with respect to the EA. Reported results are for the total meta-analysis (36,760 melanoma cases and 375,188 controls; for full details of analysis and covariates included see Online Methods ). Nevi : Associated with cutaneous melanoma+nevus count ( Online Methods ; Supplementary Table 9 ); Hair : Associated with cutaneous melanoma+hair color ( Online Methods ; Supplementary Table 10 ). Tanning response ( Tan ) and Telomere length ( Telo ) indicate lead SNP is associated with these traits when corrected for multiple testing ( Online Methods , Supplementary Table 5 ).

Article Snippet: The total meta-analysis includes self-report cutaneous melanoma GWAS data from the UK Biobank and 23andMe.

Techniques: Functional Assay

Journal: Nature genetics

Article Title: Genome-wide association meta-analyses combining multiple risk phenotypes provides insights into the genetic architecture of cutaneous melanoma susceptibility

doi: 10.1038/s41588-020-0611-8

Figure Lengend Snippet: Quantile-quantile plots of negative log 10 two sided P-value derived from a fixed-effects inverse-variance weighted meta-analysis of log(OR) effect-sizes derived from the logistic regression GWAS listed in . Only cases with histopathologically confirmed CM are included, with a total sample size of 30,134 melanoma cases and 81,415 controls.

Article Snippet: The total meta-analysis includes self-report cutaneous melanoma GWAS data from the UK Biobank and 23andMe.

Techniques: Derivative Assay

Journal: Nature genetics

Article Title: Genome-wide association meta-analyses combining multiple risk phenotypes provides insights into the genetic architecture of cutaneous melanoma susceptibility

doi: 10.1038/s41588-020-0611-8

Figure Lengend Snippet: Novel pleiotropic associations with cutaneous melanoma and nevus count or hair color. Reported cutaneous melanoma P-values are from the total fixed-effects inverse-variance weighted meta-analysis of logistic regression two-sided P-values from GWAS representing a total of 36,760 melanoma cases and 375,188 controls ( Online Methods ). Results for the lead variants from pleiotropic loci (lead SNP reaching P < 5 × 10 −8 following a Stouffers sample size weighted meta-analysis of cutaneous melanoma P-values and either Nevus GWAS meta-analysis (N = 65,777) or Hair Color GWAS (N=352,662) and GWAS-PW Model 3 prior probability of association (PPA) > 0.5, Online Methods ) distinct to those in the total cutaneous melanoma meta-analysis ( Table 1 , 2 ). CHR, BP: hg19 positional information. rsID : dbSNP142 rs number. Gene prioritizes genes that the variant is an eQTL for in GTEx skin datasets or otherwise is the closest protein coding gene; multiple indicates three or more genes. We report the total cutaneous melanoma meta-analysis P ( CM P ), and the CM+nevus or CM+hair color Stouffer’s meta-analysis fixed effect P-value. Full results can be found in Supplementary Tables 7 and 10 .

Article Snippet: The total meta-analysis includes self-report cutaneous melanoma GWAS data from the UK Biobank and 23andMe.

Techniques: Variant Assay

Journal: Nature genetics

Article Title: Genome-wide association meta-analyses combining multiple risk phenotypes provides insights into the genetic architecture of cutaneous melanoma susceptibility

doi: 10.1038/s41588-020-0611-8

Figure Lengend Snippet: LD score regression was performed for the top 4000 (A) 2000 (B) and 1000 (C) tissue-specific genes from melanocyte and GTEx tissue types (v7 datasets), to assess the enrichment of melanoma heritability in these genomic regions using summary statistics from Total CM GWAS meta-analysis. The level of enrichment and P-values are shown, with an FDR = 0.05 cutoff marked as a dashed horizontal line (See for statistical test). Tissue categories are color-coded, and a subset of top individual tissue types are shown on the plot. Tissue types from “Skin” category including melanocytes are highlighted in magenta.

Article Snippet: The total meta-analysis includes self-report cutaneous melanoma GWAS data from the UK Biobank and 23andMe.

Techniques:

Journal: Nature genetics

Article Title: Genome-wide association meta-analyses combining multiple risk phenotypes provides insights into the genetic architecture of cutaneous melanoma susceptibility

doi: 10.1038/s41588-020-0611-8

Figure Lengend Snippet: Genes identified by TWAS outside of regions identified in the total cutaneous melanoma GWAS meta-analysis. For each gene with a Bonferroni-corrected P-value cutoff in melanocytes (P TWAS < 3.22 × 10 −6 ), or skin-related tissue types (P TWAS < 5.28 × 10 −7 ) that does not overlap with an existing cutaneous melanoma region we report the local peak cutaneous melanoma variant from the total confirmed plus self-report GWAS meta-analysis, and TWAS Z score. Full results for all genes with a P TWAS < 1.48 × 10 −5 can be found in Supplementary Tables 10 , 12 . CBWD1 and C9orf66 are within 1 Mb of each other and are merged into a single locus. * RP11-676J12.7 was identified using sun-exposed skin expression data from GTEx ( Supplementary Table 12 ), while all other genes were identified using melanocyte gene expression.

Article Snippet: The total meta-analysis includes self-report cutaneous melanoma GWAS data from the UK Biobank and 23andMe.

Techniques: Variant Assay, Expressing, Gene Expression