Whole-genome sequencing in severe chronic obstructive pulmonary disease

Dmitry Prokopenko, Phuwanat Sakornsakolpat, Heide Loehlein Fier, Dandi Qiao, Margaret M. Parker, Merry Lynn N. McDonald, Ani Manichaikul, Stephen S. Rich, R. Graham Barr, Christopher J. Williams, Mark L. Brantly, Christoph Lange, Terri L Beaty, James D. Crapo, Edwin K. Silverman, Michael H. Cho

Research output: Contribution to journalArticle

Abstract

Genome-wide association studies have identified common variants associated with chronic obstructive pulmonary disease (COPD). Whole-genome sequencing (WGS) offers comprehensive coverage of the entire genome, as compared with genotyping arrays or exome sequencing. We hypothesized that WGS in subjects with severe COPD and smoking control subjects with normal pulmonary function would allow us to identify novel genetic determinants of COPD. We sequenced 821 patients with severe COPD and 973 control subjects from the COPDGene and Boston Early-Onset COPD studies, including both non-Hispanic white and African American individuals. We performed single-variant and grouped-variant analyses, and in addition, we assessed the overlap of variants between sequencing- and array-based imputation. Our most significantly associated variant was in a known region near HHIP (combined P = 1.6 3 1029); additional variants approaching genome-wide significance included previously described regions in CHRNA5, TNS1, and SERPINA6/SERPINA1 (the latter in African American individuals). None of our associations were clearly driven by rare variants, and we found minimal evidence of replication of genes identified by previously reported smaller sequencing studies. With WGS, we identified more than 20 million new variants, not seen with imputation, including more than 10,000 of potential importance in previously identified COPD genome-wide association study regions. WGS in severe COPD identifies a large number of potentially important functional variants, with the strongest associations being in known COPD risk loci, including HHIP and SERPINA1. Larger sample sizes will be needed to identify associated variants in novel regions of the genome.

Original languageEnglish (US)
Pages (from-to)614-622
Number of pages9
JournalAmerican Journal of Respiratory Cell and Molecular Biology
Volume59
Issue number5
DOIs
StatePublished - Nov 1 2018

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Pulmonary diseases
Chronic Obstructive Pulmonary Disease
Genes
Genome
Genome-Wide Association Study
African Americans
Exome
Sample Size
Smoking
Lung

Keywords

  • Association studies
  • Chronic obstructive pulmonary disease
  • Whole-genome sequencing

ASJC Scopus subject areas

  • Molecular Biology
  • Pulmonary and Respiratory Medicine
  • Clinical Biochemistry
  • Cell Biology

Cite this

Prokopenko, D., Sakornsakolpat, P., Fier, H. L., Qiao, D., Parker, M. M., McDonald, M. L. N., ... Cho, M. H. (2018). Whole-genome sequencing in severe chronic obstructive pulmonary disease. American Journal of Respiratory Cell and Molecular Biology, 59(5), 614-622. https://doi.org/10.1165/rcmb.2018-0088OC

Whole-genome sequencing in severe chronic obstructive pulmonary disease. / Prokopenko, Dmitry; Sakornsakolpat, Phuwanat; Fier, Heide Loehlein; Qiao, Dandi; Parker, Margaret M.; McDonald, Merry Lynn N.; Manichaikul, Ani; Rich, Stephen S.; Barr, R. Graham; Williams, Christopher J.; Brantly, Mark L.; Lange, Christoph; Beaty, Terri L; Crapo, James D.; Silverman, Edwin K.; Cho, Michael H.

In: American Journal of Respiratory Cell and Molecular Biology, Vol. 59, No. 5, 01.11.2018, p. 614-622.

Research output: Contribution to journalArticle

Prokopenko, D, Sakornsakolpat, P, Fier, HL, Qiao, D, Parker, MM, McDonald, MLN, Manichaikul, A, Rich, SS, Barr, RG, Williams, CJ, Brantly, ML, Lange, C, Beaty, TL, Crapo, JD, Silverman, EK & Cho, MH 2018, 'Whole-genome sequencing in severe chronic obstructive pulmonary disease', American Journal of Respiratory Cell and Molecular Biology, vol. 59, no. 5, pp. 614-622. https://doi.org/10.1165/rcmb.2018-0088OC
Prokopenko, Dmitry ; Sakornsakolpat, Phuwanat ; Fier, Heide Loehlein ; Qiao, Dandi ; Parker, Margaret M. ; McDonald, Merry Lynn N. ; Manichaikul, Ani ; Rich, Stephen S. ; Barr, R. Graham ; Williams, Christopher J. ; Brantly, Mark L. ; Lange, Christoph ; Beaty, Terri L ; Crapo, James D. ; Silverman, Edwin K. ; Cho, Michael H. / Whole-genome sequencing in severe chronic obstructive pulmonary disease. In: American Journal of Respiratory Cell and Molecular Biology. 2018 ; Vol. 59, No. 5. pp. 614-622.
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