Exome sequencing analysis in severe, early-onset chronic obstructive pulmonary disease

American Journal of Respiratory and Critical Care Medicine

Volumn 193, Issue 12, 2016, Pages 1353-1363

  Qiao, Dandi ^a   Lange, Christoph ^b   Beaty, Terri H ^c   Crapo, James D ^d   Barnes, Kathleen C ^e   Bamshad, Michael ^f   Hersh, Craig P ^a,g   Morrow, Jarrett ^a   Pinto Plata, Victor M ^h   Marchetti, Nathaniel ⁱ   Bueno, Raphael ^j   Celli, Bartolome R ^g   Criner, Gerald J ^k   Silverman, Edwin K ^a,g   Cho, Michael H ^a,g  

^a CHANNING LABORATORY   (United States)

^b HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^c JOHNS HOPKINS BLOOMBERG SCHOOL OF PUBLIC HEALTH   (United States)

^d DEPARTMENT OF MEDICINE   (United States)

^e JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^f UNIVERSITY OF WASHINGTON   (United States)

^g BOSTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^h BAYSTATE MEDICAL CENTER   (United States)

ⁱ Department of Thoracic Medicine and Surgery ^*  (United States)

^j BRIGHAM AND WOMEN S HOSPITAL   (United States)

^k TEMPLE UNIVERSITY SCHOOL OF MEDICINE   (United States)

more..

Author keywords

Chronic Obstructive Pulmonary Disease; Genetic Association Studies; Segregation Analysis

Indexed keywords

ACTIVATED LEUKOCYTE CELL ADHESION MOLECULE; DNAH8 PROTEIN; GBF1 PROTEIN; PROTEIN; RARS PROTEIN; UNCLASSIFIED DRUG;

ADULT; ARTICLE; CHRONIC OBSTRUCTIVE LUNG DISEASE; CONTROLLED STUDY; DISEASE SEVERITY; EXOME; EXOME SEQUENCING ANALYSIS; GENE EXPRESSION; GENE FREQUENCY; GENETIC ASSOCIATION; GENETIC HETEROGENEITY; HUMAN; HUMAN TISSUE; LUNG PARENCHYMA; MAJOR CLINICAL STUDY; MIDDLE AGED; PATHOGENESIS; PENETRANCE; PRIORITY JOURNAL; RNA SEQUENCE; SEGREGATION ANALYSIS; SEQUENCE ANALYSIS; SMOKING; ALPHA 1 ANTITRYPSIN DEFICIENCY; FEMALE; GENETIC PREDISPOSITION; GENETICS; GENOME-WIDE ASSOCIATION STUDY; MALE; MASSACHUSETTS; PROCEDURES; SEVERITY OF ILLNESS INDEX;

ADULT; ALPHA 1-ANTITRYPSIN DEFICIENCY; BOSTON; EXOME; FEMALE; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; HUMANS; MALE; MIDDLE AGED; PULMONARY DISEASE, CHRONIC OBSTRUCTIVE; SEVERITY OF ILLNESS INDEX;

EID: 84988909503     PISSN: 1073449X     EISSN: 15354970     Source Type: Journal    
DOI: 10.1164/rccm.201506-1223OC     Document Type: Article

References (56)

1. Mannino DM, Homa DM, Akinbami LJ, Ford ES, Redd SC. Chronic obstructive pulmonary disease surveillance-United States, 1971-2000. Respir Care 2002;47:1184-1199.
2. Hersh CP, Demeo DL, Silverman EK. Chronic obstructive pulmonary disease. In: Silverman EK, Shapiro SD, Lomas DA, Weiss ST, editors. Respiratory genetics. London: Hodder Arnold; 2005. pp. 253-296.
3. Cho MH, Boutaoui N, Klanderman BJ, Sylvia JS, Ziniti JP, Hersh CP, DeMeo DL, Hunninghake GM, Litonjua AA, Sparrow D, et al. Variants in FAM13A are associated with chronic obstructive pulmonary disease. Nat Genet 2010;42:200-202.
4. Pillai SG, Ge D, Zhu G, Kong X, Shianna KV, Need AC, Feng S, Hersh CP, Bakke P, Gulsvik A, et al.; ICGN Investigators. A genome-wide association study in chronic obstructive pulmonary disease (COPD): identification of two major susceptibility loci. PLoS Genet 2009;5: e1000421.
5. Zhou JJ, Cho MH, Castaldi PJ, Hersh CP, Silverman EK, Laird NM. Heritability of chronic obstructive pulmonary disease and related phenotypes in smokers. Am J Respir Crit Care Med 2013;188: 941-947.
6. Crosby J, Peloso GM, Auer PL, Crosslin DR, Stitziel NO, Lange LA, Lu Y, Tang ZZ, Zhang H, Hindy G, et al.; TG and HDL Working Group of the Exome Sequencing Project, National Heart, Lung, and Blood Institute. Loss-of-function mutations in APOC3, triglycerides, and coronary disease. N Engl J Med 2014;371:22-31.
7. Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, Muller J, Doerks T, Julien P, Roth A, Simonovic M, et al. STRING 8-A global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res 2009;37:D412-D416.
8. Gilissen C, Arts HH, Hoischen A, Spruijt L, Mans DA, Arts P, van Lier B, Steehouwer M, van Reeuwijk J, Kant SG, et al. Exome sequencing identifies WDR35 variants involved in Sensenbrenner syndrome. Am J Hum Genet 2010;87:418-423.
9. Flannick J, Thorleifsson G, Beer NL, Jacobs SB, Grarup N, Burtt NP, Mahajan A, Fuchsberger C, Atzmon G, Benediktsson R, et al.; Go-T2D Consortium; T2D-GENES Consortium. Loss-of-function mutations in SLC30A8 protect against type 2 diabetes. Nat Genet 2014;46: 357-363.
10. Ng SB, Buckingham KJ, Lee C, Bigham AW, Tabor HK, Dent KM, Huff CD, Shannon PT, Jabs EW, Nickerson DA, et al. Exome sequencing identifies the cause of a mendelian disorder. Nat Genet 2010;42:30-35.
11. Knowles MR, Leigh MW, Ostrowski LE, Huang L, Carson JL, Hazucha MJ, Yin W, Berg JS, Davis SD, Dell SD, et al.; Genetic Disorders of Mucociliary Clearance Consortium. Exome sequencing identifies mutations in CCDC114 as a cause of primary ciliary dyskinesia. Am J Hum Genet 2013;92:99-106.
12. Bamshad MJ, Ng SB, Bigham AW, Tabor HK, Emond MJ, Nickerson DA, Shendure J. Exome sequencing as a tool for Mendelian disease gene discovery. Nat Rev Genet 2011;12:745-755.
13. Qiao D, Lange C, Beaty TH, Crapo JD, Silverman EK, Cho MH. Whole exome sequencing analysis of severe, early-onset COPD in extended pedigrees [abstract]. Presented at the American Society of Human Genetics Conference. October 18-22, 2014, San Diego, CA
14. Qiao D, Lange C, Silverman EK, Cho MH. Whole exome sequencing analyses of severe, early-onset COPD in extended pedigrees [abstract]. Presented at the American Thoracic Society International Conference. May 16-21, 2014, San Diego, CA.
15. Silverman EK, Chapman HA, Drazen JM, Weiss ST, Rosner B, Campbell EJ, ODonnell WJ, Reilly JJ, Ginns L, Mentzer S, et al. Genetic epidemiology of severe, early-onset chronic obstructive pulmonary disease. Risk to relatives for airflow obstruction and chronic bronchitis. Am J Respir Crit Care Med 1998;157:1770-1778.
16. Lieberman J. Alpha-1-Antitrypsin deficiency and related disorders. In: Principles and practice of medical genetics, 5th ed. Vol. 2. New York: Churchill Livingstone; 1983. pp. 911-935.
17. Regan EA, Hokanson JE, Murphy JR, Make B, Lynch DA, Beaty TH, Curran-Everett D, Silverman EK, Crapo JD. Genetic epidemiology of COPD (COPDGene) study design. COPD 2010;7:32-43.
18. Kircher M, Witten DM, Jain P, ORoak BJ, Cooper GM, Shendure J. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet 2014;46:31 0-315.
19. González-Pérez A, López-Bigas N. Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score, Condel. Am J Hum Genet 2011;88: 440-449.
20. Hu H, Roach JC, Coon H, Guthery SL, Voelkerding KV, Margraf RL, Durtschi JD, Tavtigian SV, Shankaracharya, Wu W, et al. A unified test of linkage analysis and rare-variant association for analysis of pedigree sequence data. Nat Biotechnol 2014; 32:663669.
21. Lin DY, Tang ZZ. A general framework for detecting disease associations with rare variants in sequencing studies. Am J Hum Genet 2011;89:354-367.
22. Alexa A, Rahnenführer J, Lengauer T. Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics 2006;22:1600-1607.
23. Alexa A, Rahnenfuhrer J. Topgo: enrichment analysis for gene ontology, R package version 2.8. 0; 2010.
24. Exome Aggregation Consortium. Cambridge, MA: ExAC [accessed 2014 Dec]. Available from: http://exac.broadinstitute.org
25. Uhlén M, Fagerberg L, Hallström BM, Lindskog C, Oksvold P, Mardinoglu A, Sivertsson A , Kampf C, Sjöstedt E, Asplund A, et al. Proteomics: Tissue-based map of the human proteome. Science 2015;347:1260419.
26. Morrow J, Qiu W, DeMeo DL, Houston I, Pinto Plata VM, Celli BR, Marchetti N, Criner GJ, Bueno R, Washko GR, et al. Network analysis of gene expression in severe COPD lung tissue samples [abstract]. Am J Respir Crit Care Med 2015;191:A1253.
27. Cho MH, Castaldi PJ, Wan ES, Siedlinski M, Hersh CP, Demeo DL, Himes BE, Sylvia JS, Klanderman BJ, Ziniti JP, et al.; ICGN Investigators; ECLIPSE Investigators; COPDGene Investigators. A genome-wide association study of COPD identifies a susceptibility locus on chromosome 19q13. Hum Mol Genet 2012;21: 947-957.
28. Soler Artigas M, Loth DW, Wain LV, Gharib SA, Obeidat M, Tang W, Zhai G, Zhao JH, Smith AV, Huffman JE, et al.; International Lung Cancer Consortium; GIANT consortium. Genome-wide association and large-scale follow up identifies 16 new loci influencing lung function. Nat Genet 2011;43:1082-1090.
29. Wilk JB, Chen TH, Gottlieb DJ, Walter RE, Nagle MW, Brandler BJ, Myers RH, Borecki IB, Silverman EK, Weiss ST, et al. A genome-wide association study of pulmonary function measures in the Framingham Heart Study. PLoS Genet 2009;5:e1000429.
30. Cho MH, McDonald ML, Zhou X, Mattheisen M, Castaldi PJ, Hersh CP, Demeo DL, Sylvia JS, Ziniti J, Laird NM, et al.; NETT Genetics, ICGN, ECLIPSE and COPDGene Investigators. Risk loci for chronic obstructive pulmonary disease: A genome-wide association study and meta-Analysis. Lancet Respir Med 2014;2:214-225.
31. Repapi E, Sayers I, Wain LV, Burton PR, Johnson T, Obeidat M, Zhao JH, Ramasamy A, Zhai G, Vitart V, et al.; Wellcome Trust Case Control Consortium; NSHD Respiratory Study Team. Genome-wide association study identifies five loci associated with lung function. Nat Genet 2010;42:36-44.
32. Hancock DB, Eijgelsheim M, Wilk JB, Gharib SA, Loehr LR, Marciante KD, Franceschini N, van Durme YM, Chen TH, Barr RG, et al. Meta-Analyses of genome-wide association studies identify multiple loci associated with pulmonary function. Nat Genet 2010;42:45-52.
33. Wain LV, Sayers I, Soler Artigas M, Portelli MA, Zeggini E, Obeidat M, Sin DD, Bossé Y, Nickle D, Brandsma CA, et al. Whole exome re-sequencing implicates CCDC38 and cilia structure and function in resistance to smoking related airflow obstruction. PLoS Genet 2014; 10:e1004314.
34. Bowen MA, Patel DD, Li X, Modrell B, Malacko AR, Wang WC, Marquardt H, Neubauer M, Pesando JM, Francke U, et al. Cloning, mapping, and characterization of activated leukocyte-cell adhesion molecule (ALCAM), a CD6 ligand. J Exp Med 1995;181: 2213-2220.
35. Ofori-Acquah SF, King J, Voelkel N, Schaphorst KL, Stevens T. Heterogeneity of barrier function in the lung reflects diversity in endothelial cell junctions. Microvasc Res 2008;75:391-402.
36. Masedunskas A, King JA, Tan F, Cochran R, Stevens T, Sviridov D, Ofori-Acquah SF. Activated leukocyte cell adhesion molecule is a component of the endothelial junction involved in transendothelial monocyte migration. FEBS Lett 2006;580:2637-2645.
37. Kho AT, Bhattacharya S, Tantisira KG, Carey VJ, Gaedigk R, Leeder JS, Kohane IS, Weiss ST, Mariani TJ. Transcriptomic analysis of human lung development. Am J Respir Crit Care Med 2010;181:54-63.
38. Lunter PC, van Kilsdonk JW, van Beek H, Cornelissen IM, Bergers M, Willems PH, van Muijen GN, Swart GW. Activated leukocyte cell adhesion molecule (ALCAM/CD166/MEMD), a novel actor in invasive growth, controls matrix metalloproteinase activity. Cancer Res 2005; 65:8801-8808.
39. Chapelin C, Duriez B, Magnino F, Goossens M, Escudier E, Amselem S. Isolation of several human axonemal dynein heavy chain genes: genomic structure of the catalytic site, phylogenetic analysis and chromosomal assignment. FEBS Lett 1997;412:325-330.
40. Wain LV, Shrine N, Miller S, Jackson VE, Ntalla I, Artigas MS, Billington CK, Kheirallah AK, Allen R, Cook JP, et al. Novel insights into the genetics of smoking behaviour, lung function, and chronic obstructive pulmonary disease (UK BiLEVE): A genetic association study in UK Biobank. Lancet Respir Med 2015;3:769-781.
41. Kim MJ, Park BJ, Kang YS, Kim HJ, Park JH, Kang JW, Lee SW, Han JM, Lee HW, Kim S. Downregulation of FUSE-binding protein and c-myc by tRNA synthetase cofactor p38 is required for lung cell differentiation. Nat Genet 2003;34:330-336.
42. Park SG, Schimmel P, Kim S. Aminoacyl tRNA synthetases and their connections to disease. Proc Natl Acad Sci USA 2008;105: 11043-11049.
43. Claude A, Zhao BP, Kuziemsky CE, Dahan S, Berger SJ, Yan JP, Armold AD, Sullivan EM, Melançon P. GBF1: A novel Golgi-Associated BFAresistant guanine nucleotide exchange factor that displays specificity for ADP-ribosylation factor 5. J Cell Biol 1999;146:71-84.
44. Mazaki Y, Nishimura Y, Sabe H. GBF1 bears a novel phosphatidylinositolphosphate binding module, BP3K, to link PI3Kg activity with Arf1 activation involved in GPCR-mediated neutrophil chemotaxis and superoxide production. Mol Biol Cell 2012;23:2457-2467.
45. Barnes PJ. New anti-inflammatory targets for chronic obstructive pulmonary disease. Nat Rev Drug Discov 2013;12:543-559.
46. Sosnay PR, Siklosi KR, Van Goor F, Kaniecki K, Yu H, Sharma N, Ramalho AS, Amaral MD, Dorfman R, Zielenski J, et al. Defining the disease liability of variants in the cystic fibrosis transmembrane conductance regulator gene. Nat Genet 2013;45: 1160-1167.
47. Cystic fibrosis mutation database. Toronto: Cystic Fibrosis Centre at the Hospital for Sick Children; 2011.
48. Raju SV, Jackson PL, Courville CA, McNicholas CM, Sloane PA, Sabbatini G, Tidwell S, Tang LP, Liu B, Fortenberry JA, et al. Cigarette smoke induces systemic defects in cystic fibrosis transmembrane conductance regulator function. Am J Respir Crit Care Med 2013;188:1321-1330.
49. Raju SV, Tate JH, Peacock SK, Fang P, Oster RA, Dransfield MT, Rowe SM. Impact of heterozygote CFTR mutations in COPD patients with chronic bronchitis. Respir Res 2014;15:18.
50. Jørgensen AB, Frikke-Schmidt R, Nordestgaard BG, Tybjærg-Hansen A. Loss-of-function mutations in APOC3 and risk of ischemic vascular disease. N Engl J Med 2014;371:32-41.
51. de Jesus Perez VA, Yuan K, Lyuksyutova MA, Dewey F, Orcholski ME, Shuffle EM, Mathur M, Yancy L Jr, Rojas V, Li CG, et al. Wholeexome sequencing reveals TopBP1 as a novel gene in idiopathic pulmonary arterial hypertension. Am J Respir Crit Care Med 2014; 189:1260-1272.
52. Emond MJ, Louie T, Emerson J, Zhao W, Mathias RA, Knowles MR, Wright FA, Rieder MJ, Tabor HK, Nickerson DA, et al.; National Heart, Lung, and Blood Institute (NHLBI) GO Exome Sequencing Project; Lung GO. Exome sequencing of extreme phenotypes identifies DCTN4 as a modifier of chronic Pseudomonas aeruginosa infection in cystic fibrosis. Nat Genet 2012;44:886-889.
53. Ma L, Roman-Campos D, Austin ED, Eyries M, Sampson KS, Soubrier F, Germain M, Trégoue t DA, Borczuk A, Rosenzweig EB, et al. A novel channelopathy in pulmonary arterial hypertension. N Engl J Med 2013;369:351-361.
54. Ionita-Laza I, Makarov V, Yoon S, Raby B, Buxbaum J, Nicolae DL, Lin X. Finding disease variants in Mendelian disorders by using sequence data: methods and applications. Am J Hum Genet 2011; 89:701-712.
55. Wan ES, Castaldi PJ, Cho MH, Hokanson JE, Regan EA, Make BJ, Beaty TH, Han MK, Curtis JL, Curran-Everett D, et al. COPDGene Investigators. Epidemiology, genetics, and subtyping of preserved ratio impaired spirometry (PRISm) in COPDGene. Respir Res 2014; 15:89.
56. Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin) 2012; 6:80-92.