Micro-CT-Based Craniofacial Morphometrics

Reconstruction of microCT data was performed using Bruker Recon software. Hemimandible, pre-maxilla, maxilla, palatine and occipital bones were segmented and landmarks were placed using Amira software (Ho et al., 2015 (link); Welsh et al., 2018 (link)). x-y-z coordinates were imported into the R Geomorph package that was used to calculate Procrustes distances, calculate inter-landmark absolute distances and perform ANOVA statistics to determine significance. For boxplots representing inter-landmark distance measurements, a significant reduction in size of the mutant mandibles is labeled as a percentage of the wild-type mandible. Hotelling tests were performed using Procrustes transformed data, and the hotelling.test function in R. Plotting was performed in R. Numbers of embryos analyzed is indicated in the figure legends.

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Long H.K., Osterwalder M., Welsh I.C., Hansen K., Davies J.O., Liu Y.E., Koska M., Adams A.T., Aho R., Arora N., Ikeda K., Williams R.M., Sauka-Spengler T., Porteus M.H., Mohun T., Dickel D.E., Swigut T., Hughes J.R., Higgs D.R., Visel A., Selleri L, & Wysocka J. (2020). Loss of Extreme Long-Range Enhancers in Human Neural Crest Drives a Craniofacial Disorder. Cell Stem Cell, 27(5), 765-783.e14.

Publication 2020

Recon software

Anova Embryos Mandible Maxilla Microct Occipital bones Palatine Reconstruction

Corresponding Organization : Howard Hughes Medical Institute

Other organizations : Lawrence Berkeley National Laboratory, Broad Center, University of California, San Francisco, MRC Weatherall Institute of Molecular Medicine, University of Oxford, The Francis Crick Institute, Joint Genome Institute, University of California, Merced

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Variable analysis

independent variables

Mutation (wild-type vs mutant)

dependent variables

Procrustes distances
Inter-landmark absolute distances
Size of mutant mandibles (as percentage of wild-type)

control variables

Hemimandible, pre-maxilla, maxilla, palatine and occipital bones
Landmarks placed using Amira software
X-y-z coordinates imported into R Geomorph package
Hotelling tests performed using Procrustes transformed data

controls

Wild-type as positive control

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