Introduction

This project contains the steps undertaken to perform association analyses of spirometry measures in the UK Biobank (UKBB) with variants around SLC26A9 gene for patients with spirometry-defined COPD with modified GOLD criteria 2-4 of moderate to very severe lung function. The definition here is relaxed in that measurements are not required to be post-bronchodilator measurements. According to Mannino and Buist, 2007, in instances where pre-bronchodilator lung function has been recorded, an overestimate of airflow obstruction may result.

Analysis

1. 01-extract_phenos_of_interest.sh

   • input:
     • ukb24727.tab, which contains all phenotypic information from UKBB
   • output:
     • ukb24727_spirometry.tab, a smaller file containing the required variables only

2. 02-subset_qc_copd_individuals.R

   • input:
     • ukb24727_spirometry.tab
   • output:
     • ukbb_spiro_and_geno_qc.csv, which contains all the individuals passing spirometry and genotyping QC, and their spirometry measures (best FEV₁, best FVC, and FEV1pp)
     • GOLD2-4_copd_ukbb_spirodata.csv, which is the subset of individuals from ukbb_spiro_and_geno_qc.csv that fit GOLD class 2-4 criteria for lung function (i.e. FEV₁/FVC ratio < 0.7 and FEV1pp < 80%)

   This step removes individuals that did not pass spirometry and genotyping QC, removes related and non-European individuals, and calculates FEV1pp using the GLI calculator and inverse-rank normalizes the spirometry measures

3. 03-pca.sh

   • input: genotype array data for:
     • All individuals defined in GOLD2-4_copd_ukbb_spirodata.csv
     • All individuals defined in ukbb_spiro_and_geno_qc.csv
   • output:
     • 15-ukbb_copd_pcair_eigenvectors.txt for individuals corresponding to GOLD2-4_copd_ukbb_spirodata.csv
     • 18-ukbb_ukbbspiro_flashpca2_eigenvectors.txt for individuals corresponding to ukbb_spiro_and_geno_qc.csv

4. 04-assoc_spirometry.R

   • inputs:
     • ukbb_spiro_and_geno_qc.csv
     • 15-ukbb_copd_pcair_eigenvectors.txt, derived from genotyped array data from UKBB using PC-AiR from the GENESIS package (v2.16.0)
     • 18-ukbb_ukbbspiro_flashpca2_eigenvectors.txt, derived from genotyped array data from UKBB using flashPCA2 (v2.1)
     • ukb_imp_chr1_v3.bgen, which is the imputation dataset provided by UKBB
   • output:
     • ratio.irnt.assoc.csv, association results for FEV₁/FVC ratio among all 167,655 UKBB participants
     • fev1pp.irnt.assoc.csv, association results for FEV1pp among all 167,655 UKBB participants
     • ratio.irnt.assoc_copd_only.csv, association results for FEV₁/FVC ratio among all UKBB participants with spirometrically-defined COPD as per GOLD2-4 (N=14,196)
     • fev1pp.irnt.assoc_copd_only.csv, association results for FEV1pp among all 167,655 UKBB participants with spirometrically-defined COPD as per GOLD2-4 (N=14,196)
     • hasCOPD.assoc.csv, case-control association analysis of spirometrically-defined COPD cases (GOLD2-4), against those with healthy lung function (14,196 cases versus 153,459 controls)

5. merge_and_convert_to_html.py

   • inputs: the association files:
     • ratio.irnt.assoc.tsv
     • fev1pp.irnt.assoc.tsv
     • ratio.irnt.assoc_copd_only.tsv
     • fev1pp.irnt.assoc_copd_only.tsv
     • hasCOPD.assoc.tsv
   • output:
     • spirometry_in_ukbb.html for use in LocusFocus as secondary datasets to test colocalization

This step prepares the association results for loading as secondary datasets into LocusFocus

Results

The GWAS of Meconium Ileus (MI) at chr1:205,780,000-205,940,000 was tested for colocalization against the lung function phenotypic associations derived above, to test for the pleiotropic effects of this modifier locus of Cystic Fibrosis (CF) on lung function.

Colocalization was observed when the genome-wide associated peak was tested:

LocusFocus plot testing colocalization of MI GWAS with UKBB spirometry measures in all participants and in participants with COPD as per GOLD2-4 definitions. The Simple Sum colocalization region tested (gray area) was selected to match the observed peak at chr1:205,899,000-205,925,000. A total of 87 SNPs in this region were used to test for colocalization using the Simple Sum method

Colocalization results obtained are summarized in Secondary_datasets_SS_pvalues_SStest_205899-205925.csv. In short, the MI GWAS colocalizes with FEV₁/FVC ratio and COPD case-control association studies from the UKBB, and this colocalization is found to be statistically significant after multiple testing correction (-log₁₀P > 1.60).

Dataset	-log10P Colocalization
COPD case-control (N=167,655)	5.28
FEV1/FVC in UKBB (N=167,655)	7.08
FEV1pp in UKBB (N=167,655)	Did not pass first stage test
FEV1/FVC in COPD (N=14,196)	Did not pass first stage test
FEV1pp in COPD (N=14,196)	Did not pass first stage test