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Updated: May 16, 2026
13:33
Infinium Assay for Large-scale SNP Genotyping Applications
Published on: November 19, 2013
Large-scale parentage inference with SNPs: an efficient algorithm for statistical confidence of parent pair
1Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, USA.
Statistical Applications in Genetics and Molecular Biology
|November 16, 2012
Summary
New genotyping methods enable large-scale parentage inference for cultured organisms. This study introduces an efficient, likelihood-based method for assigning offspring to parent pairs using single nucleotide polymorphisms (SNPs), revolutionizing population management.
Area of Science:
- Genetics
- Population Biology
- Bioinformatics
Background:
- Advances in genotyping allow large-scale parentage inference.
- Current methods struggle with numerous potential parents.
- Intergenerational tagging is crucial for managing cultured and natural populations.
Purpose of the Study:
- To develop an efficient, likelihood-based method for parentage inference in cultured organisms.
- To enable rapid handling of a large number of potential parent pairs.
- To provide accurate statistical confidence in parentage assignments.
Main Methods:
- Developed a Markov chain representation for Mendelian incompatibilities.
- Created a fast algorithm for simulation-based confidence estimates.
- Implemented the method in the SNPPIT software.
Main Results:
- The method is efficient and accurate for large-scale parentage inference.
- 96 single nucleotide polymorphisms (SNPs) provide sufficient power to identify correct parent pairs from millions of candidates.
- Validated performance through a large simulation study on salmon populations.
Conclusions:
- The SNPPIT software and method enable fast and accurate parentage assignment in cultured organisms.
- This approach revolutionizes the management of cultured populations and scientific studies of natural populations.
- Genotyping at moderate SNP numbers is effective for large-scale parentage inference.
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