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[Preprint]. 2024 Jan 15:2024.01.12.24301204.
doi: 10.1101/2024.01.12.24301204.

Genome-wide SNP-sex interaction analysis of susceptibility to idiopathic pulmonary fibrosis

Olivia C Leavy  1   2 , Anne F Goemans  1 , Amy D Stockwell  3 , Richard J Allen  1   2 , Beatriz Guillen-Guio  1   2 , Tamara Hernandez-Beeftink  1   2 , Ayodeji Adegunsoye  4 , Helen L Booth  5 ; CleanUP-IPF Investigators of the Pulmonary Trials Cooperative; Paul Cullinan  6 , William A Fahy  7 , Tasha E Fingerlin  8 , Harvinder S Virk  2 , Ian P Hall  9   10 , Simon P Hart  11 , Mike R Hill  12 , Nik Hirani  13 , Richard B Hubbard  9   10 , Naftali Kaminski  14 , Shwu-Fan Ma  15 , Robin J McAnulty  16 , X Rebecca Sheng  3 , Ann B Millar  17 , Maria Molina-Molina  18   19   20 , Vidya Navaratnam  21   22 , Margaret Neighbors  3 , Helen Parfrey  23 , Gauri Saini  9 , Ian Sayers  24 , Mary E Strek  4 , Martin D Tobin  1   2 , Moira Kb Whyte  13 , Yingze Zhang  25 , Toby M Maher  26   27 , Philip L Molyneaux  28   26 , Justin M Oldham  29 , Brian L Yaspan  3 , Carlos Flores  30   31   20   32 , Fernando Martinez  33 , Carl J Reynolds  6 , David A Schwartz  34 , Imre Noth  15 , R Gisli Jenkins  26 , Louise V Wain  1   2
Affiliations

Genome-wide SNP-sex interaction analysis of susceptibility to idiopathic pulmonary fibrosis

Olivia C Leavy et al. medRxiv. .

Abstract

Background: Idiopathic pulmonary fibrosis (IPF) is a chronic lung condition that is more prevalent in males than females. The reasons for this are not fully understood, with differing environmental exposures due to historically sex-biased occupations, or diagnostic bias, being possible explanations. To date, over 20 independent genetic variants have been identified to be associated with IPF susceptibility, but these have been discovered when combining males and females. Our aim was to test for the presence of sex-specific associations with IPF susceptibility and assess whether there is a need to consider sex-specific effects when evaluating genetic risk in clinical prediction models for IPF.

Methods: We performed genome-wide single nucleotide polymorphism (SNP)-by-sex interaction studies of IPF risk in six independent IPF case-control studies and combined them using inverse-variance weighted fixed effect meta-analysis. In total, 4,561 cases (1,280 females and 2,281 males) and 23,500 controls (8,360 females and 14,528 males) of European genetic ancestry were analysed. We used polygenic risk scores (PRS) to assess differences in genetic risk prediction between males and females.

Findings: Three independent genetic association signals were identified. All showed a consistent direction of effect across all individual IPF studies and an opposite direction of effect in IPF susceptibility between females and males. None had been previously identified in IPF susceptibility genome-wide association studies (GWAS). The predictive accuracy of the PRSs were similar between males and females, regardless of whether using combined or sex-specific GWAS results.

Interpretation: We prioritised three genetic variants whose effect on IPF risk may be modified by sex, however these require further study. We found no evidence that the predictive accuracy of common SNP-based PRSs varies significantly between males and females.

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Conflict of interest statement

AA declares funding from NIH (K23HL146942); consulting fees from Genentech, Inogen, Medscape, Abbvie, PatientMpower and Boehringer Ingelheim; payment or honoraria for lectures, presentations, speakers bureaus, manuscript writing or educational events from Boehringer Ingelheim. ADS is a full-time employee of Genentech/Roche with stock and stock options in Roche. AFG was a full-time employee of PPD, Part of Thermo Fisher Scientific until June 2023. BGG declares fellowship funding from Wellcome Trust (221680/Z/20/Z). BLY is a full-time employee of Genentech/Roche with stock and stock options in Roche. CF declares funding Ministerio de Ciencia e Innovación, Instituto de Salud Carlos III and Instituto Tecnológico y de Energías Renovables; honoraria in educational events from Fundación Instituto Roche. DAS declares being the founder and chief scientific officer of Eleven P15, Inc., a company dedicated to the early diagnosis and treatment of pulmonary fibrosis. HP declares grant payment to institution from Boehringer Ingelheim Ltd; consulting fees from Boehringer Ingelheim Ltd, Roche Limited, Trevi Therapeutics, Pilant Therapeutics; speaker fees from Boehringer Ingelheim Ltd; member of TIPAL trial management group, trustee for Action for Pulmonary Fibrosis, member of scientific advisory board for European Pulmonary Fibrosis Federation. IN declares funding from National Institutes of Health (UG3HL145266) to institution; grant funding to institution from Veracyte; consulting fees from Boerhinger Ingelheim and Sanofi. IPH declares funding from Wellcome Trust and NIHR; vice chair Trustees for Asthma + Lung UK. JMO declares funding from National Institutes of Health (R01HL169166 & K23HL138190); consulting fees from Boehringer Ingelheim, Lupin pharmaceuticals, AmMax Bio, Roche and Veracyte; patent for TOLLIP TT genotype for NAC use in IPF; participation on a Data Safety Monitoring Board or Advisory Board for Endeavor Biomedicines, Novartis and Genentech; Associate editor for CHEST, on Program Committee for American Thoracic Society and Editorial board for AJRCCM. LVW declares funding from UK Research and Innovation (MR/V00235X/1) and GSK/Asthma + Lung UK (Professorship (C17-1)) to complete this work; funding from Orion Pharma, GSK, Genentech, AstraZeneca, Nordic Bioscience, Sysmex (OGT); Consulting fees Galapagos, Boehringer Ingelheim, GSK; support for attending meetings and/or travel Genentech; participation on Advisory Board for Galapagos; leadership or fiduciary roles as Associate Editor for European Respiratory Journal and Medical Research Council Board member and Deputy Chair. MKBW declares funding from National Institutes of Health (K23HL146942); consulting fees from Genentech, Inogen, Medscape, Abbvie, PatientMpower and Boehringer Ingelheim; payment or honoraria for lectures, presentations, speakers bureaus, manuscript writing or educational events from Boehringer Ingelheim. MN is a full-time employee of Genentech/Roche with stock and stock options in Roche. NK declares grant funding from National Institutes of Health; grant funding to institution from BMS, Boehringer Ingelheim and Three Lakes Foundation; consultancy fees from Biogen Idec, Boehringer Ingelheim, Third Rock, Pliant, Samumed, NuMedii, Theravance, Three Lake Partners, Astra Zeneca, RohBar, Veracyte, Augmanity, CSL Behring, Thyron, Gilead, Galapagos, Chiesi, Arrowhead, Sofinnova, GSK and Merk; patent for new therapies for IPF (Biotech), new therapies for ARDS (Biotech) and new Biomarkers in IPF (Biotech); equity in Pilant and Thyron; reports serving as the scientific founder of Thyron. PLM declares grant funding to institution from AstraZeneca; consultancy fees from Hoffman-La Roche, Boehringer Ingelheim, AstraZeneca, Trevi and Qureight; speaker fees from Boehringer Ingelheim and Hoffman-La Roche. RGJ declares funding from UK Research and Innovation (MR/V00235X/1); that their institute received funding from Astra Zeneca, Biogen, Galecto, GlaxoSmithKline, Nordic Biosciences, RedX and Pliant; consulting fees from AstraZeneca, Brainomix, Bristol Myers Squibb, Chiesi, Cohbar, Daewoong, GlaxoSmithKline, Veracyte, Resolution Therapeutics and Pliant; payment for lectures and presentations received from Boehringer Ingelheim, Chiesi, Roche, PatientMPower, AstraZeneca; payment for expert testimony from Pinsent Masons LLP; participation on a Data Safety Monitoring Board or Advisory Board for Boehringer Ingelheim, Galapagos, Vicore; leadership or fiduciary role for NuMedii and president for Action for Pulmonary Fibrosis. SPH declares grant funding to institution from Boehringer Ingelheim; consulting fees from Trevi therapeutics; payment or honoraria for lectures, presentations, speakers bureaus, manuscript writing or educational events from Chiesi and Trevi therapeutics; support for attending meetings and/or travel from Chiesi; Participation on a Data Safety Monitoring Board or Advisory Board for Trevi therapeutics; Chair for BTS Standards of Care Committee (till November 2022) and Trustee for Action for Pulmonary Fibrosis. TMM declares consulting fees from Boehringer Ingelheim, Roche/Genentech, Astra Zeneca, Bayer, Blade Therapeutics, Bristol-Myers Squibb, CSL Behring, Galapagos, Galecto, GlaxoSmithKline, IQVIA, Pfizer, Pliant, Respivant, Sanofi, Theravance, Trevi, Veracyte and Vicore; participation on a Data Safety Monitoring Board or Advisory Board for Fibrogen, Blade Therapeutics and Nerre. XRS is a full-time employee of Genentech/Roche with stock and stock options in Roche.

Figures

Figure 1:
Figure 1:
Overview of the SNP-by-sex interaction analysis and polygenic risk score analysis
Figure 2:
Figure 2:
Manhattan plot of meta-analysed sex-interaction results. The chromosomal position is on the x-axis and the −log(p-value) for each genetic variant in the sex-interaction meta-analysis is on the y-axis. Variants present in at least 3 studies are presented. The blue horizontal line represents the 1×10−6 p-value threshold and the red horizontal line represents 5×10−8 p-value threshold (genome-wide significance threshold).
Figure 3:
Figure 3:
Forest plots showing SNP-sex interaction odds ratio by study and the meta-analysed results for a) rs62040020, b) rs1756167317 and c) rs1663078846. OR = odds ratio and CI = confidence interval
Figure 3:
Figure 3:
Forest plots showing SNP-sex interaction odds ratio by study and the meta-analysed results for a) rs62040020, b) rs1756167317 and c) rs1663078846. OR = odds ratio and CI = confidence interval
Figure 4:
Figure 4:
Region plots for a) rs62040020, b) rs1756167317 and c) rs1663078846. The chromosomal position is on the x-axis and the −log(p-value) for each genetic variant in the sex-interaction meta-analysis is on the y-axis.
Figure 5:
Figure 5:
Forest plot for sex stratified results meta-analysed across US, Colorado, UK, UUS, CleanUP-UCD and Genentech. OR = odds ratio and CI = confidence interval
See this image and copyright information in PMC

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