Genotype probabilities at intermediate generations in the construction of recombinant inbred lines.

Genetics
Karl W Broman

Abstract

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 probabili...Continue Reading

References

Oct 26, 2000·Proceedings of the National Academy of Sciences of the United States of America·R MottJ Flint
May 2, 2003·Bioinformatics·Karl W BromanGary A Churchill
Oct 30, 2004·Nature Genetics·Gary A ChurchillUNKNOWN Complex Trait Consortium
Nov 17, 2004·Genetics·Karl W Broman
Dec 8, 2006·Genetics·Friedrich Teuscher, Karl W Broman
Jun 10, 2010·Bioinformatics·Eric Yi LiuWei Wang
Mar 10, 2011·Genetics·Frank Johannes, Maria Colomé-Tatché
Mar 17, 2011·Genome Research·David L AylorGary A Churchill
Feb 22, 2012·Genetics·UNKNOWN Collaborative Cross Consortium

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Citations

Feb 22, 2012·Genetics·David W Threadgill, Gary A Churchill
Apr 10, 2015·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·B Emma HuangColin R Cavanagh
Mar 17, 2019·G3 : Genes - Genomes - Genetics·Karl W BromanGary A Churchill
Mar 3, 2012·G3 : Genes - Genomes - Genetics·Catherine E Welsh, Leonard McMillan
Feb 22, 2012·Genetics·UNKNOWN Collaborative Cross Consortium
Mar 6, 2015·G3 : Genes - Genomes - Genetics·Chaozhi Zheng
Mar 3, 2012·G3 : Genes - Genomes - Genetics·Karl W Broman
Mar 3, 2012·G3 : Genes - Genomes - Genetics·David W Threadgill, Gary A Churchill
May 10, 2017·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Akio OhyamaTakeshi Hayashi
Jun 9, 2017·Genetics·Anuj SrivastavaFernando Pardo-Manuel de Villena
Aug 3, 2018·G3 : Genes - Genomes - Genetics·Chaozhi ZhengFred A van Eeuwijk
Nov 19, 2021·G3 : Genes - Genomes - Genetics·Karl W Broman

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Software Mentioned

R
Perl
R R Development Core Team
qtl
Maxima
HAPPY

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