Accuracy in copy number calling by qPCR and PRT: A matter of DNA

PLoS ONE

Volumn 6, Issue 12, 2011, Pages

  Fernandez Jimenez, Nora ^a,b   Castellanos Rubio, Ainara ^a,b   Plaza Izurieta, Leticia ^a,b   Gutierrez, Galder ^a   Irastorza, Iñaki ^a,b   Castaño, Luis ^a,b   Vitoria, Juan Carlos ^a,b   Bilbao, Jose Ramon ^a,b  

^a HOSPITAL DE CRUCES   (Spain)

^b UNIVERSITY OF THE BASQUE COUNTRY UPV EHU   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; ACTIN BINDING PROTEIN; BETA DEFENSIN; DEFB4A PROTEIN, HUMAN; DNA; MITOCHONDRIAL PROTEIN; PRELID1 PROTEIN, HUMAN; SYNPO PROTEIN, HUMAN;

ACCURACY; ANALYTIC METHOD; ARTICLE; CONTROLLED STUDY; DEFB4 GENE; DNA DETERMINATION; GENE; GENE DOSAGE; GENE IDENTIFICATION; GENE SEQUENCE; HUMAN; INTERMETHOD COMPARISON; PARALOG RATIO TEST; POLYMERASE CHAIN REACTION; PRELID1 GENE; PROCESS OPTIMIZATION; QUANTITATIVE STUDY; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY; SYNPO GENE; BIOASSAY; COPY NUMBER VARIATION; GENETICS; METHODOLOGY; SEQUENCE HOMOLOGY;

BETA-DEFENSINS; BIOLOGICAL ASSAY; DNA; DNA COPY NUMBER VARIATIONS; HUMANS; MICROFILAMENT PROTEINS; MITOCHONDRIAL PROTEINS; POLYMERASE CHAIN REACTION; REPRODUCIBILITY OF RESULTS; SEQUENCE HOMOLOGY, NUCLEIC ACID;

EID: 83255175577     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0028910     Document Type: Article

References (19)

1. Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, et al. (2006) Global variation in copy number in the human genome. Nature 444: 444-454.
2. Schrider DR, Hahn MW, (2010) Lower linkage disequilibrium at CNVs is due to both recurrent mutation and transposing duplications. Mol Biol Evol 27: 103-111.
3. Clayton DG, Walker NM, Smyth DJ, Pask R, Cooper JD, et al. (2005) Population structure, differential bias and genomic control in a large-scale, case-control association study. Nat Genet 37: 1243-1246.
4. Aldhous MC, Abu Bakar S, Prescott NJ, Palla R, Soo K, et al. (2010) Measurement methods and accuracy in copy number variation: failure to replicate associations of beta-defensin copy number with Crohn's disease. Hum Mol Genet 19: 4930-4938.
5. Fellermann K, Stange DE, Schaeffeler E, Schmalzl H, Wehkamp J, et al. (2006) A chromosome 8 gene-cluster polymorphism with low human beta-defensin 2 gene copy number predisposes to Crohn disease of the colon. Am J Hum Genet 79: 439-448.
6. Bentley RW, Pearson J, Gearry RB, Barclay ML, McKinney C, et al. (2010) Association of higher DEFB4 genomic copy number with Crohn's disease. Am J Gastroenterol 105: 354-359.
7. Hollox EJ, Huffmeier U, Zeeuwen PL, Palla R, Lascorz J, et al. (2008) Psoriasis is associated with increased beta-defensin genomic copy number. Nat Genet 40: 23-25.
8. Fernandez-Jimenez N, Castellanos-Rubio A, Plaza-Izurieta L, Gutierrez G, Castaño L, et al. (2010) Analysis of beta-defensin and Toll-like receptor gene copy number variation in celiac disease. Hum Immunol 71: 833-836.
9. Guescini M, Sisti D, Rocchi MB, Stocchi L, Stocchi V, (2008) A new real-time PCR method to overcome significant quantitative inaccuracy due to slight amplification inhibition. BMC Bioinformatics 30: 326-338.
10. Armour JA, Palla R, Zeeuwen PL, den Heijer M, Schalkwijk J, et al. (2007) Accurate, high-throughput typing of copy number variation using paralog ratios from dispersed repeats. Nucl Acid Res 35: e19.
11. Tahvanainen J, Kallonen T, Lähteenmäki H, Heiskanen KM, Westermarck J, et al. (2009) PRELI is a mitochondrial regulator of human primary T-helper cell apoptosis, STAT6, and Th2-cell differentiation. Blood 113: 1268-1277.
12. Asanuma K, Kim K, Oh J, Giardino L, Chabanis S, et al. (2005) Synaptopodin regulates the actin-bundling activity of alpha-actinin in anisoform-specific manner. J Clin Invest 115: 1188-1198.
13. Hollox EJ, (2008) Copy number variation of beta-defensins and relevance to disease. Cytogenet Genome Res 123: 148-155.
14. Castellanos-Rubio A, Martin-Pagola A, Santín I, Hualde I, Aransay AM, et al. (2008) Combined functional and positional gene information for the identification of susceptibility variants in celiac disease. Gastroenterology 134: 738-746.
15. Livak KJ, Schmittgen TD, (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25: 402-408.
16. Fode P, Jespersgaard C, Hardwick RJ, Bogle H, Theisen M, et al. (2011) Beta-defensin genomic copy number in different populations: a comparison of three methods. PLoS One 22: e16768.
17. Karlen Y, McNair A, Perseguers S, Mazza C, Mermod N, (2007) Statistical significance of quantitative PCR. BMC Bioinformatics 8: 131.
18. Putkonen MT, Palo JU, Cano JM, Hedman M, Sajantila A, (2010) Factors affecting the STR amplification success in poorly preserved bone simples. Inves Genet 1: 9.
19. Urban TJ, Weintrob AC, Fellay J, Colombo S, Shianna KV, et al. (2009) CCL3L1 and HIV/AIDS susceptibility. Nat Med 15: 1110-1112.