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Genotype Probabilities at Intermediate Generations in the Construction of Recombinant Inbred Lines

The mouse Collaborative Cross (CC) is a panel of eight-way recombinant inbred lines: eight diverse parental strains are intermated, followed by repeated sibling mating, many times in parallel, to create a new set of inbred lines whose genomes are random mosaics of the genomes of the original eight s...

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Autor principal: Broman, Karl W.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Genetics Society of America 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3276635/
https://www.ncbi.nlm.nih.gov/pubmed/22345609
http://dx.doi.org/10.1534/genetics.111.132647
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author Broman, Karl W.
author_facet Broman, Karl W.
author_sort Broman, Karl W.
collection PubMed
description The mouse Collaborative Cross (CC) is a panel of eight-way recombinant inbred lines: eight diverse parental strains are intermated, followed by repeated sibling mating, many times in parallel, to create a new set of inbred lines whose genomes are random mosaics of the genomes of the original eight strains. Many generations are required to reach inbreeding, and so a number of investigators have sought to make use of phenotype and genotype data on mice from intermediate generations during the formation of the CC lines (so-called pre-CC mice). The development of a hidden Markov model for genotype reconstruction in such pre-CC mice, on the basis of incompletely informative genetic markers (such as single-nucleotide polymorphisms), formally requires the two-locus genotype probabilities at an arbitrary generation along the path to inbreeding. In this article, I describe my efforts to calculate such probabilities. While closed-form solutions for the two-locus genotype probabilities could not be derived, I provide a prescription for calculating such probabilities numerically. In addition, I present a number of useful quantities, including single-locus genotype probabilities, two-locus haplotype probabilities, and the fixation probability and map expansion at each generation along the course to inbreeding.
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spelling pubmed-32766352012-02-24 Genotype Probabilities at Intermediate Generations in the Construction of Recombinant Inbred Lines Broman, Karl W. Genetics Mouse Genetic Resources The mouse Collaborative Cross (CC) is a panel of eight-way recombinant inbred lines: eight diverse parental strains are intermated, followed by repeated sibling mating, many times in parallel, to create a new set of inbred lines whose genomes are random mosaics of the genomes of the original eight strains. Many generations are required to reach inbreeding, and so a number of investigators have sought to make use of phenotype and genotype data on mice from intermediate generations during the formation of the CC lines (so-called pre-CC mice). The development of a hidden Markov model for genotype reconstruction in such pre-CC mice, on the basis of incompletely informative genetic markers (such as single-nucleotide polymorphisms), formally requires the two-locus genotype probabilities at an arbitrary generation along the path to inbreeding. In this article, I describe my efforts to calculate such probabilities. While closed-form solutions for the two-locus genotype probabilities could not be derived, I provide a prescription for calculating such probabilities numerically. In addition, I present a number of useful quantities, including single-locus genotype probabilities, two-locus haplotype probabilities, and the fixation probability and map expansion at each generation along the course to inbreeding. Genetics Society of America 2012-02 /pmc/articles/PMC3276635/ /pubmed/22345609 http://dx.doi.org/10.1534/genetics.111.132647 Text en Copyright © 2012 by the Genetics Society of America Available freely online through the author-supported open access option.
spellingShingle Mouse Genetic Resources
Broman, Karl W.
Genotype Probabilities at Intermediate Generations in the Construction of Recombinant Inbred Lines
title Genotype Probabilities at Intermediate Generations in the Construction of Recombinant Inbred Lines
title_full Genotype Probabilities at Intermediate Generations in the Construction of Recombinant Inbred Lines
title_fullStr Genotype Probabilities at Intermediate Generations in the Construction of Recombinant Inbred Lines
title_full_unstemmed Genotype Probabilities at Intermediate Generations in the Construction of Recombinant Inbred Lines
title_short Genotype Probabilities at Intermediate Generations in the Construction of Recombinant Inbred Lines
title_sort genotype probabilities at intermediate generations in the construction of recombinant inbred lines
topic Mouse Genetic Resources
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3276635/
https://www.ncbi.nlm.nih.gov/pubmed/22345609
http://dx.doi.org/10.1534/genetics.111.132647
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