Genome-wide sex interaction study summary statistics for lung function traits in UK Biobank
Creators: name: Fawcett, Katherine
name: Ma'en Obeidat
name: Melbourne, Carl
name: Shrine, Nick
name: Guyatt, Anna
name: John, Catherine
name: Jian'an Luan
name: Richmond, Anne
name: Moksnes, Marta
name: Granell, Raquel
name: Weiss, Stefan
name: Imboden, Medea
name: May-Wilson, Sebastian
name: Hysi, Pirro
name: Boutin, Thibaud
name: Portas, Laura
name: Flexeder, Claudia
name: Harris, Sarah
name: Wang, Carol
name: Leo-Pekka Lyytikäinen
name: Palviainen, Teemu
name: Foong, Rachel
name: Keidel, Dirk
name: Minelli, Cosetta
name: Langenberg, Claudia
name: Yohan Bosse
name: Berge, Maarten Van Den
name: Sin, Don
name: Hao, Ke
name: Campbell, Archie
name: Porteous, David
name: Sandosh Padmanabhan
name: Smith, Blair
name: Evans, David
name: Ring, Sue
name: Langhammer, Arnulf
name: Hveem, Kristian
name: Cristen Willer
name: Ewert, Ralf
name: Stubbe, Beate
name: Pirastu, Nicola
name: Klaric, Lucija
name: Joshi, Peter
name: Patasova, Karina
name: Mangino, Massimo
name: Polasek, Ozren
name: Starr, John M
name: Karrasch, Stefan
name: Strauch, Konstantin
name: Meitinger, Thomas
name: Rudan, Igor
name: Rantanen, Taina
name: Pietilainen, Kirsi
name: Kahonen, Mika
name: Raitakari, Olli
name: Hall, Graham
name: Sly, Peter
name: Pennell, Craig
name: Kaprio, Jaakko
name: Lehtimaki, Terho
name: Vitart, Veronique
name: Deary, Ian
name: Jarvis, Debbie
name: Wilson, James
name: Spector, Tim
name: Probst-Hensch, Nicole
name: Wareham, Nick
name: Völzke, Henry
name: Henderson, John
name: Strachan, David
name: Brumpton, Ben
name: Hayward, Caroline
name: Hall, Ian
name: Tobin, Martin
name: Wain, Louise
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: 60408 Genomics
subject: 60412 Quantitative Genetics (incl. Disease and Trait Mapping Genetics)
subject: 110311 Medical Genetics (excl. Cancer Genetics)
subject: FOS: Basic medicine
subject: FOS: Basic medicine

description: These summary statistics are derived from a genome-wide sex interaction study on spirometry-based lung function traits (forced expiratory volume in 1 second (FEV1), forced vital capacity (FVC), the ratio of FEV1 and FVC (FEV1/FVC), and peak expiratory flow (PEF) in UK Biobank. <br>Summary statistics are contained within the following files (one for each outcome). Coordinates are genome build hg19 (GRCh37).FawcettKA_prePMID_FEV1.tsv.gzFawcettKA_prePMID_FEV1_FVC_ratio.tsv.gzFawcettKA_prePMID_FVC.tsv.gzFawcettKA_prePMID_PEF.tsv.gzThe following columns are provided: variant_id, p_value, chromosome, base_pair_location, effect_allele, other_allele, effect_allele_frequency, beta, and standard_error<br>This study used anonymised data from UK Biobank (RRID: SCR_012815), which comprises over 500,000 volunteer participants aged 40-69 years recruited across Great Britain between 2006 and 2010. The protocol and consent were approved by the UK Biobank’s Research Ethics Committee. Our analysis was conducted under approved UK Biobank data application number 648. Individuals were included in this study if (i) they had no missing data for sex, age, height, and smoking status, (ii) their spirometry data passed quality control, as described previously (Shrine et al. Nat Genet. 2019;51(3):481-93. Epub 2019/02/26. doi: 10.1038/s41588-018-0321-7. PubMed PMID: 30804560; PubMed Central PMCID: PMCPMC6397078), (iii) their genetically inferred sex matched their reported sex, (iv) they had genome-wide imputed genetic data, (v) they were of genetically determined European ancestry, and (vi) they were not first- or second-degree relatives of any other individual included in the study. In total, 303,612 individuals met these criteria.<br>Participants' DNA was genotyped using either the Affymetrix Axiom(r) UK BiLEVE array or the Affymetrix Axiom(r) UK Biobank array (Bycroft et al., Nature. 2018 Oct;562(7726):203-209). Genotypes were imputed based on the Human Reference Consortium (HRC panel, as described elsewhere (Bycroft et al.). Variants with minor allele frequency (MAF)&lt;0.01 were excluded, as were variants with imputation quality scores&lt;0.3.<br>Spirometry-based lung function traits FEV1, FEV1/FVC, FVC, and PEF were pre-adjusted for age, age-squared, standing height and smoking status and the residuals rank-transformed to normality using the rntransform function of the GenABEL package (RRID: SCR_001842) in R (RRID: SCR_001905). To test each imputed autosomal variant for an interaction effect, a linear regression model with genotype (additive effect), sex, genotype-by-sex interaction, genotyping array and the first ten ancestry-based principal components included as covariates was implemented using Plink 2.0 software (RRID: SCR_001757) (https://www.cog-genomics.org/plink/2.0/).<br>For further details see the manuscript: Variants associated with HHIP expression have sex-differential effects on lung function. Wellcome Open Research.