Background: Genome-wide association studies have identified common variants associated with chronic obstructive pulmonary disease (COPD). Rare variants can also increase COPD susceptibility. Whole-genome sequencing (WGS) offers comprehensive coverage of the genome, which gives several advantages over exome sequencing, including improvements in calling of coding regions and interrogation of impactful variants in non-coding regions. We hypothesized that WGS in subjects with severe COPD and smoking controls with preserved pulmonary function would allow us to identify novel genetic determinants for COPD and resistance to smoking effects.
Methods: As part of the NHLBI Trans‐Omics for Precision Medicine (TOPMed) program, we submitted DNA samples for sequencing from 600 severely affected white and 330 African-American (AA) COPD cases with a mean forced expiratory volume in 1 second (FEV1) of 32% and 35% predicted, respectively. Current and ex-smoker controls (500 white and 570 AA) had FEV1> 85%. Samples were sequenced at > 30x coverage using PCR-free libraries, with centralized mapping and variant calling by the University of Michigan Informatics Research Core. We adjusted for population substructure using the rare variant Jaccard method and grouped variants into non-overlapping windows using a spatial clustering approach. We performed preliminary single-variant and region-based analysis both genome-wide and in candidate genes. We further assessed the overlap of variants between sequencing and imputation using reference panels.
Results: We performed an initial analysis in 1794 subjects. The populations were analyzed separately and a combined analysis of both groups was performed. We confirmed a known region near HHIP (combined p=1.6x10-9) and identified near-significant variants near TNS1 in whites and SERPINA1 in AA. In 22 loci recently described as genome-wide significant in COPD, we found several nominally significant regions in SKAT-O analysis (MAF < 1%). A comparison of these regions found 62,248 variants in non-Hispanic whites not present in the Haplotype Resource Consortium Imputation, and 147,815 variants in African-Americans not present in the 1000 Genomes cosmopolitan imputation, including 17,542 variants with MAF > 5%..
Conclusions: Whole-genome sequencing can identify large numbers of potentially functional and deleterious variants, and will serve as an important resource for identifying causal variants at known and novel loci for COPD. Future plans include association tests in the larger sample for affection status and COPD-related phenotypes and also for fine-mapping.
Funding: This work was supported by NHLBI R01 HL084323, P01 HL114501, P01 HL105339 and R01 HL089856 (E.K.S.); R01 HL113264 (M.H.C. and E.K.S.), and R01 HL089897 (J.D.C.). The COPDGene study (NCT00608764) is also supported by the COPD Foundation through contributions made to an Industry Advisory Board comprised of AstraZeneca, Boehringer Ingelheim, Novartis, Pfizer, GlaxoSmithKline, Siemens and Sunovion.

Background: Genome-wide association studies have identified common variants associated with chronic obstructive pulmonary disease (COPD). Rare variants can also increase COPD susceptibility but have been challenging to identify. While exome sequencing has traditionally been performed to identify rare disease variants, whole-genome sequencing (WGS) offers several advantages, including potentially improved accuracy in coding regions and interrogation of non-coding regions. We hypothesize that WGS in subjects with severe COPD and smoking controls with preserved pulmonary function will allow us to identify novel genetic determinants for COPD.
Methods: As part of the NHLBI Trans‐Omics for Precision Medicine (TOPMed) program, we submitted 2000 subjects for WGS. COPDGene non-Hispanic white (Nhw, 500) and African-American (AA, 330) cases had severe (GOLD spirometry grade 3-4) COPD with a median forced expiratory volume in 1 second (FEV1) of 35% and 39% predicted, respectively. Current and ex-smoker controls (500 Nhw and 570 Aa) had FEV1 > 85%. One hundred probands from the Boston-Early Onset COPD Study (EOCOPD) had a median FEV1 of 20% predicted. Samples were sequenced at > 30x coverage on the Illumina X10 through the University of Washington using PCR-free libraries, with centralized mapping and variant calling by the University of Michigan Informatics Research Core. We assessed characteristics of variants in pre-defined regions using SNPEff and the combined annotation dependent depletion (CADD) score.
Results: To date, we have received whole genome sequencing data on 692 samples. The overall concordance rate with existing array genotyping exceeded 99%. After removing 3 mismatched subjects, we identified a total of 41,819,809 single nucleotide variants, of which 10,010,421 were novel (not previously described in dbSnp144) in 46 EOCOPD cases, 144 COPDGene Nhw cases and 151 controls, and 112 AA cases and 236 controls. Within a set of 129 genes from Mendelian diseases associated with COPD or emphysema, or at loci from genome-wide association studies of COPD or lung function, we identified 1870 nonsynonymous, stop, or splice variants, including 50 putative loss-of-function variants. In 500kb regions around each of six genome-wide significant regions from a recent study of COPD, we identified 813 putatively deleterious non-coding variants based on a CADD score of > 15.
Conclusions: Whole-genome sequencing can identify large numbers of potentially functional and deleterious variants, and will serve as an important resource for identifying causal variants at known and novel loci. Future plans include association tests for affection status and for secondary phenotypes including imaging and transcriptomics data.
Funding: This work was supported by NHLBI R01 HL084323, P01 HL083069, P01 HL105339 and R01 HL089856 (E.K.S.); R01 HL113264 (M.H.C. and E.K.S.), and R01 HL089897 (J.D.C.). The COPDGene study (NCT00608764) is also supported by the COPD Foundation through contributions made to an Industry Advisory Board comprised of AstraZeneca, Boehringer Ingelheim, Novartis, Pfizer, GlaxoSmithKline, Siemens and Sunovion.