Genetic Mapping of Mouse Brain Size

GigaMUGA and MegaMUGA genotyping of recombinants was performed by GeneSeek (Neogen; Lincoln, NE). Quality and intensity normalization of the SNP data was checked using routines provided in the R-package Argyle [51 (link)]. Linkage mapping, including scanone and scantwo analyses, was performed on informative SNP markers and brain sizes (mm²) of ninety-six F₂ recombinants using the R/qtl software package (Broman 2003; Broman and Sen 2009). Threshold levels of significance were established using at least 1,000 permutations of the respective dataset.
Coding differences of candidate genes were compared using the Mouse Genomes Project website from Wellcome Sanger Trust Institute (https://www.sanger.ac.uk/sanger/Mouse_SnpViewer/rel-1211, NCBIm37).

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Snedeker J., Gibbons WJ J.r., Paulding D.F., Abdelhamed Z., Prows D.R, & Stottmann R.W. (2019). Gpr63 is a modifier of microcephaly in Ttc21b mouse mutants. PLoS Genetics, 15(11), e1008467.

Publication 2019

GeneSeek

Brain Genes permutations Genomes Mouse

Corresponding Organization : Shriners Hospitals for Children - Cincinnati

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Variable analysis

independent variables

GigaMUGA and MegaMUGA genotyping of recombinants

dependent variables

Brain sizes (mm^2) of ninety-six F2 recombinants

control variables

Quality and intensity normalization of the SNP data was checked using routines provided in the R-package Argyle
Linkage mapping, including scanone and scantwo analyses, was performed on informative SNP markers

controls

Threshold levels of significance were established using at least 1,000 permutations of the respective dataset

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