From Schemalet Wiki

Contents 1 Links 1.1 Reporting protocols 1.2 Check list for a meta study 1.3 Study/investigation specific metadata 1.4 Marker specific metadata

Links

Reporting protocols

• STrengthening the REporting of Genetic Association Studies (STREGA)— An Extension of the STROBE Statement

Check list for a meta study

The list is compiled from data specifications used in ENGAGE meta studies

Study/investigation specific metadata

variable	description	example
id	submittor id
model	study model	bmi ~ sex + age +additive(SNP)
phenotype	name of phenotype	bmi
sample set	type of sample set	cohort
design	study design ?	whole sample set
samples	number of samples in study	do we need also number of cases and controls ?
gender	gender of samples	M, F or M+F
datatype	type of data	imputed or direct
instrument	name of instrument	Illumina
chip	name of array chip	HumanHap300
software	name of software used in allele calling ?	BeadStudio/Illuminus
exp.software	name of software used in association study?	GenABEL/PLINK
build	genome build version	36
exp. processing type	?	standard
adj. & stand.	?	z-score adjusted

Marker specific metadata

variable	description	example
name	name of marker	rs1212212
chromosome	name of chromosome	X
position	location of marker in base pairs	12345
strand	orientation on strand	either + or -
allele1	allele 1	A, T, C, G or 0 (zero) for missing data
allele2	allele 2	as above
effallele	effective allele	either A,T,C,G or 0 as above
effallelefreq	frequency of effective allele	0.66
n	number of samples having effective allele ??	100
beta	estimate of the effect of the "effective" allele	(in additive model)
sebeta	standard error of the estimate
p	probability value for disease association	1.0e-5
pgc-lambda	genomic control inflation factor
phwe	p-value for Hardy-Weinber equilibrium
calling rate	success rate