ResultsSharingFormat

Results Sharing

The following variables should be included when sharing imputed results for meta-analysis; large files can be shared among small groups via secure file transfer site (as described in Results Sharing). Many working groups use ShareSpaces, a secure web-based file-sharing system implemented by the University of Washington's Catalyst computing group. The service has ample storage space for large files and limits access to a select group identified by UW Netids, or by Google Account IDs. 

ShareSpace Access is arranged via working groups. New members who expect to need access to these sites should create a Google Account ID: create a new Google Account (more information).

File Formats

Results should be shared as plain text files, with the following variable names:

variable name	description
SNPID	SNP ID as rs number
chr	chromosome number. Use symbols X, XY, Y and mt for non-autosomal markers.
position	physical position for the reference sequence (indicate build 35/36 in readme file)
coded_all	coded allele, also called modeled allele (in example of A/G SNP in which AA=0, AG=1 and GG=2, the coded allele is G)
noncoded_all	the other allele
strand_genome	+ or -, representing either the positive/forward strand or the negative/reverse strand of the human genome reference sequence; to clarify which strand the coded_all and noncoded_all are on
beta	beta estimate from genotype-phenotype association, at least 5 decimal places -- “NA” if not available
SE	standard error of beta estimate, to at least 5 decimal places -- “NA” if not available
pval	p-value of test statistic, here just as a double check -- “NA” if not available
AF_coded_all	allele frequency for the coded allele -- “NA” if not available
HWE_pval	exact test Hardy-Weinberg equilibrium p-value -- only directly typed SNPs, NA for imputed
callrate	genotyping callrate after exclusions
n_total	total sample with phenotype and genotype for SNP
imputed	1/0 coding; 1=imputed SNP, 0=if directly typed
used_for_imp	1/0 coding; 1=used for imputation, 0=not used for imputation
oevar_imp	observed divided by expected variance for imputed allele dosage

Please note that a README should be uploaded with a very brief description of the data uploaded, the date, the NCBI human genome reference sequence used (e.g. NCBI 36.2) for strand reference, and the scale of the beta estimates; please also include in the README the SNP HWE p-value, callrate and minor allele frequency filters that have been applied.

For gene-environment interaction analyses, the following variables should be included:

variable name	description
SNPID	SNP ID as rs number
chr	chromosome number. Use symbols X, XY, Y and mt for non-autosomal markers.
position	physical position for the reference sequence (indicate build 35/36 in readme file)
coded_all	coded allele, also called modeled allele (in example of A/G SNP in which AA=0, AG=1 and GG=2, the coded allele is G)
noncoded_all	the other allele
strand_genome	+ or -, representing either the positive/forward strand or the negative/reverse strand of the human genome reference sequence; to clarify which strand the coded_all and noncoded_all are on
beta	beta estimate from additive interaction term, at least 5 decimal places -- “NA” if not available
SE	standard error of beta estimate, to at least 5 decimal places -- “NA” if not available
pval	p-value of interaction test statistic, here just as a double check -- “NA” if not available
df.t	degrees of freedom estimate for t reference distribution for interaction term -- “NA” if not available
pval.t	p-value of interaction test statistic, using t reference distribution, here just as a double check -- “NA” if not available
beta.main	beta estimate from genotype-phenotype association, at least 5 decimal places -- “NA” if not available
SE.main	standard error of beta.main estimate, to at least 5 decimal places -- “NA” if not available
pval.main	p-value of main test statistic, here just as a double check -- “NA” if not available
covar.main.inter	covariance between beta and beta.main, to at least 5 decimal places  -- “NA” if not available
AF_coded_all	allele frequency for the coded allele -- “NA” if not available
HWE_pval	exact test Hardy-Weinberg equilibrium p-value -- only directly typed SNPs, NA for imputed
callrate	genotyping callrate after exclusions
n_total	total sample with phenotype and genotype for SNP
n_exposed	(DICHOTOMOUS EXPOSURE ONLY) number in sample exposed to environmental variable of interest [in longitudinal data, estimated number of independent observations that are exposed]
imputed	1/0 coding; 1=imputed SNP, 0=if directly typed
used_for_imp	1/0 coding; 1=used for imputation, 0=not used for imputation
oevar_imp	observed divided by expected variance for imputed allele dosage

Please note that a README should be uploaded with a very brief description of the data uploaded, the date, the NCBI human genome reference sequence used (e.g. NCBI 36.2) for strand reference, and the scale of the beta estimates; please also include in the README the SNP HWE p-value, callrate and minor allele frequency filters that have been applied.