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Published on: July 27, 2021
PREST-plus identifies pedigree errors and cryptic relatedness in the GAW18 sample using genome-wide SNP data
Lei Sun1, Apostolos Dimitromanolakis2
1Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Canada ; Department of Statistical Sciences, University of Toronto, Canada.
This study used PREST-plus on genetic data to find pedigree errors and cryptic relatedness in family studies. The analysis successfully identified mis-specified relationships and previously unknown genetic connections among individuals.
Area of Science:
- Genetics
- Bioinformatics
- Population Studies
Background:
- Pedigree errors and cryptic relatedness are common in genetic studies.
- These issues can negatively impact linkage and association analyses, leading to inaccurate results.
Purpose of the Study:
- To identify pedigree errors and cryptic relatedness within the San Antonio Family Studies (SAFS) cohort.
- To assess the utility of the PREST-plus tool for detecting such genetic discrepancies.
Main Methods:
- Application of the PREST-plus software to genome-wide single-nucleotide polymorphism (SNP) data.
- Analysis of estimated identity-by-descent (IBD) distributions for all pairwise comparisons of genotyped individuals.
- Comparison of genotype-derived relatedness with pedigree information.
Main Results:
- PREST-plus identified 7 mis-specified relative pairs based on genotype data, showing significant deviations in IBD estimates.
- The tool detected 4 instances of cryptic relatedness involving 7 individuals across 6 families.
- Initial pedigree analysis alone predicted numerous related pairs, highlighting the need for genotype verification.
Conclusions:
- PREST-plus is effective in detecting pedigree errors and cryptic relatedness using SNP data.
- Accurate identification of genetic relationships is crucial for the validity of genetic association and linkage studies.
- The findings underscore the importance of rigorous quality control in genetic family studies.
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