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The APL test: extension to general nuclear families and haplotypes and examination of its robustness.

Publication ,  Journal Article
Chung, R-H; Hauser, ER; Martin, ER
Published in: Hum Hered
2006

OBJECTIVE: The Association in the Presence of Linkage test (APL) is a powerful statistical method that allows for missing parental genotypes in nuclear families. However, in its original form, the statistic does not easily extend to mixed nuclear family structures nor to multiple-marker haplotypes. Furthermore, the robustness of APL in practice has not been examined. Here we present a generalization of the APL model and examination of its robustness under a variety of non-standard scenarios. METHODS: The generalization is made possible by incorporating a bootstrap variance estimator instead of the original robust variance estimator. This allows for use of more than two affected siblings. Haplotype analysis was accomplished by combining estimation of haplotype phase into the EM algorithm. Computer simulation was used to examine robustness of the APL to departures from test assumptions. RESULTS: The extended APL tests both single-marker and multiple-marker haplotypes and shows more power than other association methods. Simulation results showed that the single-marker APL test is robust to the departure from HWE. For the haplotype test, violation of the HWE assumption can inflate type I error. We also evaluated general guidelines for the validity of APL with rare alleles and rare haplotypes. Software for the APL test is available from http://www.chg.duke.edu/research/apl.html.

Duke Scholars

Published In

Hum Hered

DOI

ISSN

0001-5652

Publication Date

2006

Volume

61

Issue

4

Start / End Page

189 / 199

Location

Switzerland

Related Subject Headings

  • Models, Genetic
  • Linkage Disequilibrium
  • Humans
  • Haplotypes
  • Genetics & Heredity
  • Gene Frequency
  • Data Interpretation, Statistical
  • Computer Simulation
  • 3105 Genetics
  • 0604 Genetics
 

Citation

APA
Chicago
ICMJE
MLA
NLM
Chung, R.-H., Hauser, E. R., & Martin, E. R. (2006). The APL test: extension to general nuclear families and haplotypes and examination of its robustness. Hum Hered, 61(4), 189–199. https://doi.org/10.1159/000094774
Chung, Ren-Hua, Elizabeth R. Hauser, and Eden R. Martin. “The APL test: extension to general nuclear families and haplotypes and examination of its robustness.Hum Hered 61, no. 4 (2006): 189–99. https://doi.org/10.1159/000094774.
Chung, Ren-Hua, et al. “The APL test: extension to general nuclear families and haplotypes and examination of its robustness.Hum Hered, vol. 61, no. 4, 2006, pp. 189–99. Pubmed, doi:10.1159/000094774.
Journal cover image

Published In

Hum Hered

DOI

ISSN

0001-5652

Publication Date

2006

Volume

61

Issue

4

Start / End Page

189 / 199

Location

Switzerland

Related Subject Headings

  • Models, Genetic
  • Linkage Disequilibrium
  • Humans
  • Haplotypes
  • Genetics & Heredity
  • Gene Frequency
  • Data Interpretation, Statistical
  • Computer Simulation
  • 3105 Genetics
  • 0604 Genetics