Genetica

, Volume 134, Issue 2, pp 187–197

Assessment of power and accuracy of methods for detection and frequency-estimation of null alleles

Article

DOI: 10.1007/s10709-007-9224-8

Cite this article as:
Girard, P. & Angers, B. Genetica (2008) 134: 187. doi:10.1007/s10709-007-9224-8

Abstract

Null alleles represent a common artefact of microsatellite-based analyses. Rapid methods for their detection and frequency estimation have been proposed to replace the existing time-consuming laboratory methods. The objective of this paper is to assess the power and accuracy of these statistical tools using both simulated and real datasets. Our results revealed that none of the tests developed to detect null alleles are perfect. However, combining tests allows the detection of null alleles with high confidence. Comparison of the estimators of null allele frequency indicated that those that account for unamplified individuals, such as the Brookfield2 estimator, are more accurate than those that do not. Altogether, the use of statistical tools appeared more appropriate than testing with alternative primers as null alleles often remain undetected following this laborious work. Based on these results, we propose recommendations to detect and correct datasets with null alleles.

Keywords

Detection tests Estimators Heterozygosity Null alleles Power Sample size 

Abbreviations

CI

Confidence interval

FNULL

Null allele frequency (parameter of the frequency distribution)

\(\hat{F}_{\text{NULL}} \)

Null allele frequency (estimation from a sample)

HE-TOT

Heterozygosity calculated with both null and visible alleles (parameter)

ĤE-TOT

Heterozygosity calculated with both null and visible alleles (estimation)

HE-VIS

Heterozygosity calculated with visible alleles only (parameter)

ĤE-VIS

Heterozygosity calculated with visible alleles only (estimation)

HO

Frequency of individuals having two visible alleles (parameter)

ĤO

Frequency of individuals having two visible alleles (estimation)

HWE

Hardy–Weinberg equilibrium

k

Total number of alleles

MCT

Micro-checker test

NVIS

Number of individuals having at least one visible allele (parameter)

\(\hat{N}_{\text{VIS}} \)

Number of individuals having at least one visible allele (estimation)

PCR

polymerase chain reaction

rCHAK

Null allele frequency estimation according to the Chakraborty estimator

rBROOK1

Null allele frequency estimation according to the Brookfield1 estimator

rBROOK2

Null allele frequency estimation according to the Brookfield2 estimator

TBR2

Brookfield2 test

UT

U-test

Copyright information

© Springer Science+Business Media B.V. 2007

Authors and Affiliations

  1. 1.GRIL, Département des Sciences BiologiquesUniversité de MontréalMontrealCanada

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