CNVrd, a Read-Depth Algorithm for Assigning Copy-Number at the FCGR Locus: Population-Specific Tagging of Copy Number Variation at FCGR3B

PLoS ONE

Volumn 8, Issue 4, 2013, Pages

  Nguyen, Hoang tan ^a   Merriman, Tony R ^a   Black, Michael A ^a  

^a UNIVERSITY OF OTAGO   (New Zealand)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; COPY NUMBER VARIATION; FCGR2A GENE; FCGR2B GENE; FCGR2C GENE; FCGR3A GENE; FCGR3B GENE; GENE; GENE DUPLICATION; GENE LOCUS; GENETIC ALGORITHM; GENETIC ANALYSIS; HUMAN; MICROARRAY ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; VALIDATION STUDY; ALGORITHM; GENE FREQUENCY; GENETICS; GENOTYPE; HAPLOTYPE MAP; INTERNET; NUCLEIC ACID DATABASE; REPRODUCIBILITY;

FC RECEPTOR; FCGR3B PROTEIN, HUMAN; GLYCOSYLPHOSPHATIDYLINOSITOL ANCHORED PROTEIN;

ALGORITHMS; DATABASES, NUCLEIC ACID; DNA COPY NUMBER VARIATIONS; GENE FREQUENCY; GENETIC LOCI; GENOTYPE; GPI-LINKED PROTEINS; HAPMAP PROJECT; HUMANS; INTERNET; POLYMORPHISM, SINGLE NUCLEOTIDE; RECEPTORS, IGG; REPRODUCIBILITY OF RESULTS;

EID: 84877005022     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0063219     Document Type: Article

References (37)

1. Merikangas AK, Corvin AP, Gallagher L, (2009) Copy-number variants in neurodevelopmental disorders: promises and challenges. Trends Genet 25: 536-544.
2. Wellcome Trust Case Control Consortium, (2010) Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls. Nature. 464: 713-720.
3. Bentley RB, Pearson J, Gearry RB, Barclay ML, McKinney C, et al. (2010) Association of higher DEFB4 copy number with Crohn's disease. Am J Gastroenterol 105: 354-359.
4. McKinney C, Merriman ME, Chapman PT, Gow PJ, Harrison AA, et al. (2008) Evidence for an influence of chemokine ligand 3-like 1 (CCL3L1) gene copy number on susceptibility to rheumatoid arthritis. Ann Rheum Dis 67: 409-413.
5. McKinney C, Fanciulli M, Merriman M, Phipps-Green A, Alizadeh B, et al. (2010) Association of variation in Fc Gamma Receptor 3B (FCGR3B) gene copy number with rheumatoid arthritis in Caucasian samples. Ann Rheum Dis 69: 1711-1716.
6. McKinney C, Merriman TR, (2012) Meta-analysis confirms a role for deletion in FCGR3B in autoimmune phenotypes. Hum Mol Genet 21: 2370-2376.
7. Mamtani M, Anaya JM, He W, Ahuja SK, (2010) Association of copy number variation in the FCGR3B gene with risk of autoimmune diseases. Genes Immun 11: 155-160.
8. Niederer HA, Willcocks LC, Rayner TF, Yang W, Lau YL,et al. (2010) Copy number, linkage disequilibrium and disease association in the FCGR locus. Hum Mol Genet 19, 3282-3294.
9. Yang Y, Chung EK, Wu YL, Savelli SL, Nagaraja HN, et al. (2007) Gene copy-number variation and associated polymorphisms of complement component C4 in human systemic lupus erythematosus (SLE): low copy number is a risk factor for and high copy number is a protective factor against SLE susceptibility in European Americans. Am J Hum Genet 80: 1037-1054.
10. Zhou XJ, Lv JC, Bu DF, Yu L, Yang YR, et al. (2010) Copy number variation of FCGR3A rather than FCGR3B and FCGR2B is associated with susceptibility to anti-GBM disease. Int Immunol 22: 45-51.
11. Robinson JI, Carr IM, Cooper DL, Rashid LH, Martin SG, et al. (2012) Confirmation of association of FCGR3B but not FCGR3A copy number with susceptibility to autoantibody positive rheumatoid arthritis. Hum Mutation 33: 741-749.
12. McKinney C, Broen JCA, Vonk MC, Beretta L, Hesselstrand R, et al. (2012) Evidence that deletion at FCGR3B is a risk factor for systemic sclerosis. Genes Immun 13: 458-460.
13. Cukier HN, Pericak-Vance MA, Gilbert JR, Hedges DJ, (2009) Sample degradation leads to false-positive copy number variation calls in multiplex real-time polymerase chain reaction assays. Anal Biochem 386: 288-290.
14. Hollox EJ, Detering JC, Dehnugara T, (2009) An integrated approach for measuring copy number variation at the FCGR3 (CD16) locus. Hum Mutation 30: 477-484.
15. Fernandez-Jimenez N, Castellanos-Rubio A, Plaza-Izurieta L, Gutierrez G, Irastorza I, et al. (2011) Accuracy in copy number calling by qPCR and PRT: a matter of DNA. PLoS One 6: e28910.
16. Field SF, Howson JM, Maier LM, Walker S, Walker NM, et al. (2009) Experimental aspects of copy number variant assays at CCL3L1. Nat Med 15: 1115-1117.
17. Hollox EJ, (2010) Beta-defensins and Crohn's disease: confusion from counting copies. Am J Gastroenterol 105: 360-362.
18. Abyzov A, Urban AE, Snyder M, Gerstein M, (2011) CNVnator: An approach to discover, genotype and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res 21: 974-984.
19. Breunis WB, van Mirre E, Geissler J, Laddach N, Wolbink G, et al. (2009) Copy number variation at the FCGR locus includes FCGR3A, FCGR2C and FCGR3B but not FCGR2A and FCGR2B. Hum Mutation 30: E640-E650.
20. Colobran R, Pedrosa E, Carretero-Iglesia L, Juan M, (2010) Copy number variation in chemokine superfamily: the complex scene of CCL3L-CCL4L genes in health and disease. Clin Exp Immunol 162: 41-52.
21. Li H, Durbin R, (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
22. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079.
23. Yoon S, Xuan Z, Makarov V, Ye K, Sebat J, (2009) Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Res 19: 1586-1592.
24. Venkatraman ES, Olshen AB, (2007) A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics 23: 657-663.
25. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, et al. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5: R80.
26. Danecek P, Auton A, Abecasis G, Albers CA, Banks E, et al. (2011) The variant call format and VCF tools. Bioinformatics 27: 2156-2158.
27. Li H, (2011) Tabix: fast retrieval of sequence features from generic TAB-delimited files. Bioinformatics 27: 718-719.
28. Fredman D, White SJ, Potter S, Eichler EE, Den Dunnen JT, et al. (2004) Complex SNP-related sequence variation in segmental genome duplications. Nat Genet 36: 861-864.
29. Agresti A, (1992) A survey of exact inference for contingency tables. Statistical Sci 7: 131-137.
30. Benjamini Y, Hochberg Y, (1995) Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. J Royal Stat Soc Series B 57: 289-300.
31. McCarroll SA, Kuruvilla FG, Korn JM, Cawley S, Nemesh J, et al. (2008) Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat Genet 40: 1166-1174.
32. Conrad DF, Pinto D, Redon R, Feuk L, Gokcumen O, et al. (2010) Origins and functional impact of copy number variation in the human genome. Nature 464: 704-712.
33. Armour JA, Palla R, Zeeuwen PL, Den Heijer M, Shalkwijk J, et al. (2007) Accurate, high-throughput typing of copy number variation using paralogue ratios from dispersed repeats. Nucl Acids Res 35: e19.
34. Campbell CD, Sampas N, Tsalenko A, Sudmant PH, Kidd JM, et al. (2011) Population-genetic properties of differentiated human copy-number polymorphisms. Am J Hum Genet 88: 317-332.
35. Alkan C, Kidd JM, Marques-Bonet T, Aksay G, Antonacci F, et al. (2009) Personalized copy number and segmental duplication maps using next-generation sequencing. Nat Genet 41: 1061-1067.
36. Waszak SM, Hasin Y, Zichner T, Olender T, Keydar I, et al. (2010) Systematic inference of copy-number genotypes from personal genome sequencing data reveals extensive olfactory receptor gene content diversity. PLoS Comput Biol 6: e1000988.
37. Klambauer G, Schwarzbauer K, Mayr A, Clevert D-A, Mitterecker A, et al. (2012) cn.MPOS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate. Nucl Acids Res 40: e69.