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APIS: An auto-adaptive parentage inference software that tolerates missing parents.

Ronan Griot1,2, François Allal3, Sophie Brard-Fudulea1

  • 1SYSAAF, Station LPGP/INRA, Rennes, France.

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|October 15, 2019
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Summary

APIS is a new R package for parentage assignment using genomic data. It accurately assigns offspring to parents without prior information, even with missing parent genotypes and high error rates.

Keywords:
SNPmicrosatellitesmissing parentsparentage assignmentpedigree

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Area of Science:

  • Genetics
  • Bioinformatics
  • Computational Biology

Background:

  • Parentage assignment using genomic markers faces challenges like genotyping errors and missing parent data.
  • Existing software often requires prior estimates of error rates and missing parent proportions.
  • These limitations impact the reliability of parentage assignment in genetic studies.

Purpose of the Study:

  • Introduce the R package APIS for parentage assignment.
  • Develop a method that does not require prior estimates of genotyping errors or missing parent proportions.
  • Provide a user-defined acceptable error rate for assignments.

Main Methods:

  • APIS utilizes Mendelian transmission probabilities to establish assignment rules.
  • It estimates the proportion of offspring with missing parental genotypes.
  • The package was compared against CERVUS and VITASSIGN using European seabass SNP data.

Main Results:

  • APIS demonstrated a lower type I error rate (false positives) compared to other software, particularly with missing parental genotypes.
  • While the true positive rate was sometimes lower, APIS met user-set error rates (1% or 5%) even with simulated high genotyping errors and up to 50% missing sires.
  • The software is best suited for large datasets with over 200 offspring.

Conclusions:

  • APIS is a reliable and user-friendly tool for parentage assignment.
  • It effectively handles missing parental genotypes and genotyping errors.
  • The package is particularly advantageous for studies with numerous offspring and potential data gaps.