High-Throughput Genotyping for Genetic Variance

Following genotyping, five DNA samples per each wild-type (WT), Neo/+, WT/−, Neo/Neo, and Neo/− groups were sent to GeneSeek Inc. (a NeoGene company, Lincoln, Nebraska USA). DNA samples were run on the GigaMuga mouse genotyping chips (Illumina), for a total of 143,000 SNPs. After quality control and removal of the X and Y chromosomes, we performed analyses using 133,559 SNPs on each of 17 samples, 4–5 per group. QC and SNP calls were done using the GenomeStudio Package (Illumina) by GeneSeek. Further analysis was performed using the SNPRelate Package in R to calculate the SNP frequencies and the relative inbreeding^{69 (link)}. The SNP frequencies were used to calculate the additive genetic variance⁷⁰.

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Green R.M., Fish J.L., Young N.M., Smith F.J., Roberts B., Dolan K., Choi I., Leach C.L., Gordon P., Cheverud J.M., Roseman C.C., Williams T.J., Marcucio R.S, & Hallgrímsson B. (2017). Developmental nonlinearity drives phenotypic robustness. Nature Communications, 8, 1970.

Publication 2017

GenomeStudio Package

Chips Mouse Type dna Y chromosomes

Corresponding Organization :

Other organizations : Alberta Children's Hospital, University of Calgary, University of Massachusetts Lowell, University of California, San Francisco, University of Colorado Anschutz Medical Campus, Loyola University Chicago, University of Illinois Urbana-Champaign

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Variable analysis

independent variables

Genotype groups (WT, Neo/+, WT/−, Neo/Neo, Neo/−)

dependent variables

SNP frequencies
Relative inbreeding
Additive genetic variance

control variables

Quality control and removal of X and Y chromosomes
SNP calls using the GenomeStudio Package (Illumina) by GeneSeek

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