Difference between revisions of "GIANT consortium data files"

From Giant Consortium
Jump to navigation Jump to search
m (spell out BMI)
(file description added)
Line 2: Line 2:
  
  
We are releasing the summary data from our 2010 meta-analyses of GWA data, in order to enable other researchers to examine particular variants or loci for their evidence of association with anthropometric traits. The files include p-values and direction of effect at over 2 million directly genotyped or imputed single nucleotide polymorphisms (SNPs). To prevent the possibility of identification of individuals from these summary results, we are not releasing allele frequency data from our samples. A manuscript describing the rationale for releasing association data but not frequency data is in preparation.
+
We are releasing the summary data from our 2010 meta-analyses of Genome-wide Association (GWA) data, in order to enable other researchers to examine particular variants or loci for their evidence of association with anthropometric traits. The files include p-values and direction of effect at over 2 million directly genotyped or imputed single nucleotide polymorphisms (SNPs). To prevent the possibility of identification of individuals from these summary results, we are not releasing allele frequency data from our samples. A manuscript describing the rationale for releasing association data but not frequency data is in preparation.
 +
 
 +
 
 +
'''Data file description:'''
 +
 
 +
Each file consists of the following information for each SNP and its association to the specified trait based on meta-analysis in the respective publication. SNPs where N < 50% of the maximum have been excluded.
 +
 
 +
;MarkerName  :The [http://www.ncbi.nlm.nih.gov/SNP/ dbSNP] name of the genetic marker
 +
;Allele1      :The first allele, by definition the trait-increasing allele (hg18 + strand)
 +
;Allele2      :The second allele (hg18 + strand)
 +
;Freq.Allele1.HapMapCEU    :The allele frequency of Allele1 in the [http://www.hapmap.org HapMap] CEU population
 +
;p            :P value after meta-analysis using regression coefficients (beta and standard error), and after correction for inflation of test statistics using genomic control both at the individual study level and again after meta-analysis
 +
;N            :Number of observations
  
  

Revision as of 13:21, 1 July 2011

GIANT consortium GWAS metadata is available here for download.

We are releasing the summary data from our 2010 meta-analyses of Genome-wide Association (GWA) data, in order to enable other researchers to examine particular variants or loci for their evidence of association with anthropometric traits. The files include p-values and direction of effect at over 2 million directly genotyped or imputed single nucleotide polymorphisms (SNPs). To prevent the possibility of identification of individuals from these summary results, we are not releasing allele frequency data from our samples. A manuscript describing the rationale for releasing association data but not frequency data is in preparation.


Data file description:

Each file consists of the following information for each SNP and its association to the specified trait based on meta-analysis in the respective publication. SNPs where N < 50% of the maximum have been excluded.

MarkerName
The dbSNP name of the genetic marker
Allele1
The first allele, by definition the trait-increasing allele (hg18 + strand)
Allele2
The second allele (hg18 + strand)
Freq.Allele1.HapMapCEU
The allele frequency of Allele1 in the HapMap CEU population
p
P value after meta-analysis using regression coefficients (beta and standard error), and after correction for inflation of test statistics using genomic control both at the individual study level and again after meta-analysis
N
Number of observations


BMI (download GZIP)

MD5 (GIANT_BMI_Speliotes2010_publicrelease_HapMapCeuFreq.txt -- 79 MB; 2,471,517 lines) = 38c836542807a3830101bcf48bb34472

If you use these Body Mass Index data, please cite: Speliotes, E.K., Willer, C.J., Berndt, S.I., Monda, K.L., Thorleifsson, G., Jackson, A.U., Allen, H.L., Lindgren, C.M., Luan, J., Magi, R., et al. (2010). Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index. Nat Genet 42, 937-948.


Height (download GZIP)

MD5 (GIANT_HEIGHT_LangoAllen2010_publicrelease_HapMapCeuFreq.txt -- 82 MB; 2,469,636 lines) = b51b4c4ff1f03bd33c4b2dfd6b10cb82

If you use these height data, please cite: Lango Allen, H., Estrada, K., Lettre, G., Berndt, S.I., Weedon, M.N., Rivadeneira, F., Willer, C.J., Jackson, A.U., Vedantam, S., Raychaudhuri, S., et al. (2010). Hundreds of variants clustered in genomic loci and biological pathways affect human height. Nature 467, 832-838.


WHRadjBMI (download GZIP)

MD5 (GIANT_WHRadjBMI_Heid2010_publicrelease_HapMapCeuFreq.txt -- 75 MB; 2,483,326 lines) = 8f7e2ca61c33a120db9e7bfe51e3c053

If you use these waist-hip ratio adjusted for BMI data, please cite: Heid, I.M., Jackson, A.U., Randall, J.C., Winkler, T.W., Qi, L., Steinthorsdottir, V., Thorleifsson, G., Zillikens, M.C., Speliotes, E.K., Magi, R., et al. (2010). Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution. Nat Genet 42, 949-960.