SUMMARY: Results for a genetic association study of four smoking behaviour related traits
PAPER: Erzurumluoglu, Liu, Jackson et al, 2019. Meta-analysis of up to 622,409 individuals identifies 40 novel smoking behaviour associated genetic loci. Molecular Psychiatry
CORRESPONDENCE: Joanna Howson, University of Cambridge (jmmh2@medschl.cam.ac.uk) and Dajiang Liu, Penn State University (dxl46@psu.edu)
 
TRAITS: SI: Smoking Initiation; CPD: Cigarettes per day; PY: Pack years; SC: Smoking cessation
SAMPLE SIZE (discovery+replication samples): Total sample size for SI is up to 622,409 individuals for SNPs that are on both the Exome-chip and the UK Biobank Axiom chip (~40k overlapping SNPs). We removed variants with N < 40,000 for PY and N < 50,000 for SC, SI and CPD. Most SNPs will have a sample size of ~400k - as these will have been genotyped on the Axiom (or UK BiLEVE) array only.
SOFTWARE: RAREMETAL (https://genome.sph.umich.edu/wiki/RAREMETAL_Documentation)
 
FILE NAMES:
Erzurumluoglu_et_al_2018_combined_meta-analysis_SI_results_02132019.txt.gz - gzipped text file with SI association results for 1,210,805 genetic variants (discovery+replication samples)
Erzurumluoglu_et_al_2018_combined_meta-analysis_CPD_results_02132019.txt.gz - gzipped text file with CPD association results for 1,208,949 genetic variants (discovery+replication samples)
Erzurumluoglu_et_al_2018_discovery-stage_meta-analysis_PY_results_02132019.txt.gz - gzipped text file with PY association results for 931,028 genetic variants (discovery samples only)
Erzurumluoglu_et_al_2018_combined_meta-analysis_SC_results_02132019.txt.gz - gzipped text file with SC association results for 934,972 genetic variants (discovery+replication samples)
 
OUTPUT LEGEND:
CHROM:              Chromosome Name
POS:                Variant Position (hg19 build 37)
REF:                Reference Allele
ALT:                Alternative Allele
N:		    Sample size for SNP (this is currently problematic for some SNPs as Exome-chip SNPs that were not on the Axiom array were counted as monomorphic - when in reality they were not genotyped for those studies)
ALT_ALLELE_FREQ:    Frequency of variant in 1000G. (NA if unavailable)
NUMBER_OF_STUDIES:  Number of Studies that have contributed to this variant (similar issue with sample size where some were counted as contributing when it was actually monomorphic)
EFFECT_SIZE:        Alternative Allele Effect Size
EFFECT_SIZE_SD:	    Standard error
H2:		    SNP heritability estimate
PVALUE:		    P-value
GTEx_ID: 	    Genotype-Tissue Expression ID
rsID:		    Reference SNP cluster ID