Whole-exome sequencing of a pedigree segregating asthma

BMC Medical Genetics

Volumn 13, Issue , 2012, Pages

  DeWan, Andrew T ^a   Egan, Kathryn Brigham ^b   Hellenbrand, Karen ^b   Sorrentino, Keli ^b   Pizzoferrato, Nicole ^a   Walsh, Kyle M ^a,c   Bracken, Michael B ^b  

^a YALE UNIVERSITY   (United States)

^b YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Asthma; CBLB; KALRN; PDE4DIP; Whole exome sequencing

Indexed keywords

E3 UBIQUITIN LIGEASE CBL B; KALIRIN; MEMBRANE PROTEIN; MYOMEGALIN; PHOSPHODIESTERASE; SALBUTAMOL; UBIQUITIN PROTEIN LIGASE E3; UNCLASSIFIED DRUG;

ADOLESCENT; ADULT; ARTICLE; ASTHMA; CHILD; CLINICAL ARTICLE; CONTROLLED STUDY; EXOME; FAMILY; FATHER; FEMALE; GENE EXPRESSION; GENE IDENTIFICATION; GENE SEGREGATION; GENETIC ASSOCIATION; GENETIC DATABASE; GENETIC VARIABILITY; HUMAN; MALE; MOTHER; PEDIGREE; PROGENY; RISK FACTOR; SCHOOL CHILD; SCORING SYSTEM; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; WHOLE EXOME SEQUENCING;

ADOLESCENT; ADULT; ALLELES; ASTHMA; CHILD; EXOME; FEMALE; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HUMANS; MALE; MIDDLE AGED; PEDIGREE; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; YOUNG ADULT;

EID: 84867114056     PISSN: None     EISSN: 14712350     Source Type: Journal    
DOI: 10.1186/1471-2350-13-95     Document Type: Article

References (40)

1. Moffatt MF, Kabesch M, Liang L, Dixon AL, Strachan D, Heath S, Depner M, von Berg A, Bufe A, Rietschel E, et al. Genetic variants regulating ORMDL3 expression contribute to the risk of childhood asthma. Nature 2007, 448(7152):470-473.
2. Moffatt MF, Gut IG, Demenais F, Strachan DP, Bouzigon E, Heath S, von Mutius E, Farrall M, Lathrop M, Cookson WO. A large-scale, consortium-based genomewide association study of asthma. N Engl J Med 2010, 363(13):1211-1221.
3. Himes BE, Hunninghake GM, Baurley JW, Rafaels NM, Sleiman P, Strachan DP, Wilk JB, Willis-Owen SA, Klanderman B, Lasky-Su J, et al. Genome-wide association analysis identifies PDE4D as an asthma-susceptibility gene. Am J Hum Genet 2009, 84(5):581-593.
4. Li X, Howard TD, Zheng SL, Haselkorn T, Peters SP, Meyers DA, Bleecker ER. Genome-wide association study of asthma identifies RAD50-IL13 and HLA-DR/DQ regions. J Allergy Clin Immunol 2010, 125(2):328-335. e311.
5. Sleiman PM, Flory J, Imielinski M, Bradfield JP, Annaiah K, Willis-Owen SA, Wang K, Rafaels NM, Michel S, Bonnelykke K, et al. Variants of DENND1B associated with asthma in children. N Engl J Med 2010, 362(1):36-44.
6. Hancock DB, Romieu I, Shi M, Sienra-Monge JJ, Wu H, Chiu GY, Li H, del Rio-Navarro BE, Willis-Owen SA, Weiss ST, et al. Genome-wide association study implicates chromosome 9q21.31 as a susceptibility locus for asthma in mexican children. PLoS Genet 2009, 5(8):e1000623.
7. Gudbjartsson DF, Bjornsdottir US, Halapi E, Helgadottir A, Sulem P, Jonsdottir GM, Thorleifsson G, Helgadottir H, Steinthorsdottir V, Stefansson H, et al. Sequence variants affecting eosinophil numbers associate with asthma and myocardial infarction. Nat Genet 2009, 41(3):342-347.
8. Maher B. Personal genomes: The case of the missing heritability. Nature 2008, 456(7218):18-21.
9. Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, McCarthy MI, Ramos EM, Cardon LR, Chakravarti A, et al. Finding the missing heritability of complex diseases. Nature 2009, 461(7265):747-753.
10. Eichler EE, Flint J, Gibson G, Kong A, Leal SM, Moore JH, Nadeau JH. Missing heritability and strategies for finding the underlying causes of complex disease. Nat Rev Genet 2010, 11(6):446-450.
11. Maller J, George S, Purcell S, Fagerness J, Altshuler D, Daly MJ, Seddon JM. Common variation in three genes, including a noncoding variant in CFH, strongly influences risk of age-related macular degeneration. Nat Genet 2006, 38(9):1055-1059.
12. Sanna S, Jackson AU, Nagaraja R, Willer CJ, Chen WM, Bonnycastle LL, Shen H, Timpson N, Lettre G, Usala G, et al. Common variants in the GDF5-UQCC region are associated with variation in human height. Nat Genet 2008, 40(2):198-203.
13. Weedon MN, Lettre G, Freathy RM, Lindgren CM, Voight BF, Perry JR, Elliott KS, Hackett R, Guiducci C, Shields B, et al. A common variant of HMGA2 is associated with adult and childhood height in the general population. Nat Genet 2007, 39(10):1245-1250.
14. Lee SH, Park JS, Park CS. The search for genetic variants and epigenetics related to asthma. Allergy Asthma Immunol Res 2011, 3(4):236-244.
15. McClellan J, King MC. Genetic heterogeneity in human disease. Cell 2010, 141(2):210-217.
16. DeWan A, Triche E, Xu X, Hsu L-I, Zhao C, Belanger K, Hellenbrand K, Willis-Owen SA, Moffat M, Cookson W, et al. PDE11A associations with asthma: results of a genome-wide association scan. Journal of Allergy & Clinical Immunology 2010, 126(4):871-873.
17. Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 2010, 26(5):589-595.
18. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The sequence alignment/map format and SAMtools. Bioinformatics 2009, 25(16):2078-2079.
19. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, et al. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 2010, 20(9):1297-1303.
20. DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 2011, 43(5):491-498.
21. Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res 2010, 38(16):e164.
22. Liu X, Jian X, Boerwinkle E. dbNSFP: a lightweight database of human nonsynonymous SNPs and their functional predictions. Hum Mutat 2011, 32(8):894-899.
23. Murk W, Walsh K, Hsu LI, Zhao L, Bracken MB, Dewan AT. Attempted replication of 50 reported asthma risk genes identifies a SNP in RAD50 as associated with childhood atopic asthma. Hum Hered 2011, 71(2):97-105.
24. Neale BM, Kou Y, Liu L, Ma'ayan A, Samocha KE, Sabo A, Lin CF, Stevens C, Wang LS, Makarov V, et al. Patterns and rates of exonic de novo mutations in autism spectrum disorders. Nature 2012, 485(7397):242-245.
25. Sanders SJ, Murtha MT, Gupta AR, Murdoch JD, Raubeson MJ, Willsey AJ, Ercan-Sencicek AG, DiLullo NM, Parikshak NN, Stein JL, et al. De novo mutations revealed by whole-exome sequencing are strongly associated with autism. Nature 2012, 485(7397):237-241.
26. Verde I, Pahlke G, Salanova M, Zhang G, Wang S, Coletti D, Onuffer J, Jin SL, Conti M. Myomegalin is a novel protein of the golgi/centrosome that interacts with a cyclic nucleotide phosphodiesterase. J Biol Chem 2001, 276(14):11189-11198.
27. Uys GM, Ramburan A, Loos B, Kinnear CJ, Korkie LJ, Mouton J, Riedemann J, Moolman-Smook JC. Myomegalin is a novel A-kinase anchoring protein involved in the phosphorylation of cardiac myosin binding protein C. BMC Cell Biol 2011, 12:18.
28. Naramura M, Jang IK, Kole H, Huang F, Haines D, Gu H. c-Cbl and Cbl-b regulate T cell responsiveness by promoting ligand-induced TCR down-modulation. Nat Immunol 2002, 3(12):1192-1199.
29. Ionita-Laza I, Perry GH, Raby BA, Klanderman B, Lee C, Laird NM, Weiss ST, Lange C. On the analysis of copy-number variations in genome-wide association studies: a translation of the family-based association test. Genet Epidemiol 2008, 32(3):273-284.
30. Walsh KM, Bracken MB, Murk WK, Hoh J, Dewan AT. Association between reduced copy-number at T-cell receptor gamma (TCRgamma) and childhood allergic asthma: a possible role for somatic mosaicism. Mutat Res 2010, 690(1-2):89-94.
31. Zhang W, Kuncewicz T, Yu ZY, Zou L, Xu X, Kone BC. Protein-protein interactions involving inducible nitric oxide synthase. Acta Physiol Scand 2003, 179(2):137-142.
32. Batra J, Pratap Singh T, Mabalirajan U, Sinha A, Prasad R, Ghosh B. Association of inducible nitric oxide synthase with asthma severity, total serum immunoglobulin E and blood eosinophil levels. Thorax 2007, 62(1):16-22.
33. Tennessen JA, Bigham AW, O'Connor TD, Fu W, Kenny EE, Gravel S, McGee S, Do R, Liu X, Jun G, et al. Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science 2012, 337(6090):64-69.
34. Nelson MR, Wegmann D, Ehm MG, Kessner D, St Jean P, Verzilli C, Shen J, Tang Z, Bacanu SA, Fraser D, et al. An abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people. Science 2012, 337(6090):100-104.
35. Wang L, Fan C, Topol SE, Topol EJ, Wang Q. Mutation of MEF2A in an inherited disorder with features of coronary artery disease. Science 2003, 302(5650):1578-1581.
36. de Quervain DJ, Poirier R, Wollmer MA, Grimaldi LM, Tsolaki M, Streffer JR, Hock C, Nitsch RM, Mohajeri MH, Papassotiropoulos A. Glucocorticoid-related genetic susceptibility for Alzheimer's disease. Hum Mol Genet 2004, 13(1):47-52.
37. Bhagavatula MR, Fan C, Shen GQ, Cassano J, Plow EF, Topol EJ, Wang Q. Transcription factor MEF2A mutations in patients with coronary artery disease. Hum Mol Genet 2004, 13(24):3181-3188.
38. Weng L, Kavaslar N, Ustaszewska A, Doelle H, Schackwitz W, Hebert S, Cohen JC, McPherson R, Pennacchio LA. Lack of MEF2A mutations in coronary artery disease. J Clin Invest 2005, 115(4):1016-1020.
39. Yang Y, Dowling J, Yu QC, Kouklis P, Cleveland DW, Fuchs E. An essential cytoskeletal linker protein connecting actin microfilaments to intermediate filaments. Cell 1996, 86(4):655-665.
40. Edvardson S, Cinnamon Y, Jalas C, Shaag A, Maayan C, Axelrod FB, Elpeleg O. Hereditary sensory autonomic neuropathy caused by a mutation in dystonin. Ann Neurol 2012, 71(4):569-572.