Detection of genotyping errors by Hardy-Weinberg equilibrium testing

European Journal of Human Genetics

Volumn 12, Issue 5, 2004, Pages 395-399

  Hosking, Louise ^a   Lumsden, Sheena ^a   Lewis, Karen ^a   Yeo, Astrid ^a   McCarthy, Linda ^a   Bansal, Aruna ^a   Riley, John ^a   Purvis, Ian ^a   Xu, Chun Fang ^a  

^a GLAXOSMITHKLINE   (United Kingdom)

Author keywords

Error; Genotyping; Hardy Weinberg equilibrium

Indexed keywords

DNA;

ANALYTIC METHOD; ANALYTICAL EQUIPMENT; ANALYTICAL ERROR; ARTICLE; BIOASSAY; CONTROLLED STUDY; DATA ANALYSIS; GENE FREQUENCY; GENE SEQUENCE; GENETIC ANALYSIS; GENOTYPE; HIGH THROUGHPUT SCREENING; HUMAN; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; PRIORITY JOURNAL; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM;

DNA; GENE FREQUENCY; GENOTYPE; HUMANS; LINKAGE DISEQUILIBRIUM; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

EID: 2442650305     PISSN: 10184813     EISSN: None     Source Type: Journal    
DOI: 10.1038/sj.ejhg.5201164     Document Type: Article

References (36)

1. Douglas JA, Boehnke M, Lange K: A multipoint method for detecting genotyping errors and mutations in sibling-pair linkage data. Am J Hum Genet 2000; 66: 1287-1297.
2. Gordon D, Heath SC, Ott J: True pedigree errors more frequent than apparent errors for single nucleotide polymorphisms. Hum Hered 1999; 49: 65-70.
3. Ewen KR, Bahlo M, Treloar SA et al: Identification and analysis of error types in high-throughput genotyping. Am J Hum Genet 2000; 67: 727-736.
4. Sobel E, Papp JC, Lange K: Detection and integration of genotyping errors in statistical genetics. Am J Hum Genet 2002; 70: 496-508.
5. Abecasis GR, Cherny SS, Cardon L: The impact of genotyping error on family based analysis of quantitative traits. Eur J Hum Genet 2001; 9: 130-134.
6. Terwilliger JD, Weeks DE, Ott J: Laboratory errors in the reading of marker alleles cause massive reductions in lod score and lead to gross over-estimations of the recombination fraction. Am J Hum Genet 1990; 47: A201.
7. Gordon D, Matise TC, Heath SC, Ott J: Power loss for multiallelic transmission/disequilibrium test when errors introduced: GAW11 simulated data. Genet Epidemiol 1999; 17 (Suppl 1): S587-S592.
8. Gordon D, Finch SJ, Nothnagel M, Ott J: Power and sample size calculations for case:control genetic association tests when errors are present: application to single nucleotide polymorphisms. Hum Hered 2002; 54: 22-33.
9. Ehm MG, Kimmel M, Cottingham RW: Error detection for genetic data, using likelihood methods. Am J Hum Genet 1996; 58: 225-234.
10. Douglas JA, Skol AD, Boehnke M: Probability of detection of genotyping errors and mutations as inheritance inconsistencies in nuclear-family data. Am J Hum Genet 2002; 70: 487-495.
11. Ott J: Linkage analysis with misclassification at one locus. Clin Genet 1977; 12: 119-124.
12. Goldstein DR, Zhao H, Speed TP: The effects of genotyping errors and interference on estimation of genetic distance. Hum Hered 1997; 47: 86-100.
13. Cherny SS, Abecasis GR, Cookson WO, Sham P, Cardon L: The effect of genotype and pedigree error on linkage analysis: analysis of three asthma genome scans. Genet Epidemiol 2001; 25: 36-47.
14. O'Connell JR: Genotyping and error checking. in Elston R, Olson J, Palmer L (eds): Biostatistical Genetics and Genetic Epidemiology. New York: Wiley; 2002, pp 348-352.
15. Beutow KH: Influence of aberrant observations on high resolution linkage analysis outcomes. Am J Hum Genet 1991; 49: 985-994.
16. Shields DC, Collins A, Buetow KH, Morton NE: Error filtration, interference and the human linkage map. Proc Nat Acad Sci USA 1991; 88: 6501-6505.
17. Mitchell AA, Cutler DJ, Chakravarti A: Undetected genotyping errors cause apparent overtransmission of common alleles in the transmission/disequilibrium test. Am J Hum Genet 2003; 72: 598-610.
18. Gordon D, Leal SM, Heath SC, Ott J: An analytical solution to sinlge nucleotide polymorphism error-detection rates in nuclear families: implications for study design. Pac Symp Biocomput 2000; 663-674.
19. Gordon D, Ott J: Assessment and management of single nucleotide polymorphism genotype errors in genetic association analysis. Pac Symp Biocomput 2001; 18-29.
20. Akey JM, Zhang K, Xiong M, Doris P, Jin L: The effect that genotyping errors have on the robustness of common linkage disequilibrium measures. Am J Hum Genet 2001; 68: 1447-1456.
21. Mote VL, Anderson RL: An investigation of the effect of misclassification on the properties of chi-square tests in the analysis of categorical data. Biometrika 1965; 52: 95-109.
22. Gordon D, Levenstein MA, Finch SJ, Ott J: Errors and linkage disequilibrium interact multiplicatively when computing sample sizes for genetic case-control association studies. Pac Symp Biocomput 2003; 490-501.
23. Goring HH, Terwilliger JD: Linkage analysis in the presence of errors I: complex valued recombination fractions and complex phenotypes. Am J Hum Genet 2000; 66: 1095-1106.
24. Goring HH, Terwilliger JD: Linkage analysis in the presence of errors II: marker-locus genotyping errors modelled with hypercomplex recombination fractions. Am J Hum Genet 2000; 66: 1107-1108.
25. Goring HH, Terwilliger JD: Linkage analysis in the presence of errors III: marker loci and their map as nuisance parameters. Am J Hum Genet 2000; 66: 1298-1309.
26. Goring HH, Terwilliger JD: Linkage analysis in the presence of errors IV: joint pseudomarker analysis of linkage and/or linkage disequilibrium on a mixture of pedigrees and singletons when the mode of inheritance cannot be accurately specified. Am J Hum Genet 2000; 66: 1310-1327.
27. Gordon D, Heath SC, Liu X, Ott J: A transmission disequilibrium test that allows for genotyping errors in the analysis of single nucleotide polymorphism data. Am J Hum Genet 2001; 69: 371-380.
28. Rice KM, Holmans P: Allowing for genotyping error in analysis of unmatched cases and controls. Ann Hum Genet 2003; 67: 165-174.
29. Hardy GH: Mendelian proportions in a mixed population. Science 1908; 28: 49-50.
30. McCarthy LC, Hosford DA, Riley JH et al: Single nucleotide polymorphism alleles in the insulin receptor gene are associated with typical migraine. Genomics 2001; 78: 135-149.
31. Hewett D, Samuelsson L, Polding J et al: Identification of a psoriasis susceptibility gene by linkage disequilibrium mapping with a localised single nucleotide polymorphism map. Genomics 2002; 79: 305-314.
32. Hosking LK, Boyd PR, Xu C-F et al: Linkage disequilibrium mapping identifies a 390 kb region associated with CYP2D6 poor drug metabolising activity. Pharmacogenomics J 2002; 2: 165-175.
33. Benjamini Y, Hochberg Y: Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Statist Soc B 1995; 57: 289-300.
34. Ranade K, Chang M-S, Ting C-T et al: High-throughput genotyping with single nucleotide polymorphisms. Genet Res 2001; 11: 1262-1268.
35. Harrison PM, Hegyi H, Balasubramanian S et al: Molecular fossils in the human genome identification and analysis of the pseudogenes in chromosomes 21 and 22. Genet Res 2002; 12: 272-280.
36. Bailey J, Gu Z, Clark R et al: Recent segmental duplications in the human genome. Science 2002; 297: 1003-1007.