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Genotypic Inference of HIV-1 Tropism Using Population-based Sequencing of V3
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Parentage assignment with genotyping-by-sequencing data.

Andrew Whalen1, Gregor Gorjanc1, John M Hickey1

  • 1The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK.

Journal of Animal Breeding and Genetics = Zeitschrift Fur Tierzuchtung Und Zuchtungsbiologie
|December 15, 2018
PubMed
Summary
This summary is machine-generated.

Genotyping-by-sequencing (GBS) effectively assigns parentage, even with low-coverage data, by using a large number of markers. This method, AlphaAssign, offers a robust alternative to traditional array data for genetic analysis.

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Area of Science:

  • Genetics
  • Bioinformatics
  • Population Genetics

Background:

  • Traditional parentage assignment relies on array data.
  • Genotyping-by-sequencing (GBS) offers a cost-effective alternative but presents challenges with low coverage and variable sequencing depth.
  • Accurate genotype calling is crucial for parentage assignment.

Purpose of the Study:

  • To evaluate the efficacy of genotype-by-sequencing (GBS) data for parentage assignment.
  • To address challenges associated with low-coverage GBS data and variable sequencing depth.
  • To develop and validate a novel probabilistic framework for parentage assignment using GBS data.

Main Methods:

  • Extended a probabilistic framework to compare noisy GBS genotypes against proposal distributions of expected genotype probabilities for relatives.
  • Developed the AlphaAssign program for parentage assignment.
  • Evaluated the method using simulated data with varying GBS coverage levels.

Main Results:

  • High-coverage (>2×) GBS data performed comparably to array data, requiring fewer markers for accurate parentage assignment.
  • Low-coverage GBS data (as low as 0.1×) successfully assigned parentage when a large number of markers were utilized.
  • A high false positive rate with low-coverage GBS data was observed when the true parent was absent from candidate lists, but this was reducible by adjusting the assignment threshold.

Conclusions:

  • Genotyping-by-sequencing (GBS) is a viable and effective method for parentage assignment, even with low-coverage data.
  • The developed AlphaAssign program provides a robust tool for parentage assignment using GBS data.
  • Careful consideration of marker numbers and assignment thresholds is necessary for optimizing accuracy, especially with low-coverage GBS data.