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FSuite: exploiting inbreeding in dense SNP chip and exome data
Steven Gazal1, Mourad Sahbatou2, Marie-Claude Babron1
1Inserm, U946, Genetic variability and human diseases, Paris, 75010, Université Paris Sud, Kremlin-Bicêtre, 94270, Fondation Jean Dausset CEPH, Paris, 75010, Université Paris-Diderot, UMR 946, Institut Universitaire d'Hématologie, Paris, 75475, Inserm, U1078, Génétique, Génomique fonctionnelle et Biotechnologies, Brest, 29218 and Centre Hospitalier Régional Universitaire de Brest, Brest, 29200, France Inserm, U946, Genetic variability and human diseases, Paris, 75010, Université Paris Sud, Kremlin-Bicêtre, 94270, Fondation Jean Dausset CEPH, Paris, 75010, Université Paris-Diderot, UMR 946, Institut Universitaire d'Hématologie, Paris, 75475, Inserm, U1078, Génétique, Génomique fonctionnelle et Biotechnologies, Brest, 29218 and Centre Hospitalier Régional Universitaire de Brest, Brest, 29200, France.
FSuite is a new pipeline that analyzes human genomic data to identify inbreeding. It aids in detecting inbred individuals and mapping homozygous regions for genetic studies.
Area of Science:
- Genomics
- Population Genetics
- Bioinformatics
Background:
- Inbreeding information from human genomic data is crucial for genetic studies.
- Existing software may lack comprehensive tools for analyzing inbreeding.
- Human genetic data, including single nucleotide polymorphism (SNP) chip and exome data, can reveal inbreeding patterns.
Purpose of the Study:
- To introduce FSuite, a user-friendly pipeline for exploiting inbreeding information in human genomic data.
- To provide a complete suite of scripts for describing and utilizing inbreeding data.
- To facilitate the identification of inbred individuals, mating types, and shared homozygous regions.
Main Methods:
- FSuite is a pipeline developed in Perl.
- It utilizes R functions for generating graphical outputs.
- The software processes single nucleotide polymorphism (SNP) chip or exome data.
Main Results:
- FSuite includes modules for detecting inbred individuals and estimating inbreeding coefficients.
- It can describe mating type proportions and individual probabilities of offspring.
- The pipeline enables homozygosity mapping to identify shared regions between affected individuals.
Conclusions:
- FSuite offers a comprehensive solution for analyzing inbreeding in human genomic data.
- It supports population genetic studies by characterizing mating patterns.
- FSuite aids in identifying rare recessive mutations associated with diseases through homozygosity mapping.
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