The FaceBase Consortium: A comprehensive resource for craniofacial researchers

Abstract

The FaceBase Consortium, funded by the National Institute of Dental and Craniofacial Research, National Institutes of Health, is designed to accelerate understanding of craniofacial developmental biology by generating comprehensive data resources to empower the research community, exploring high-throughput technology, fostering new scientific collaborations among researchers and human/computer interactions, facilitating hypothesis-driven research and translating science into improved health care to benefit patients. The resources generated by the FaceBase projects include a number of dynamic imaging modalities, genome-wide association studies, software tools for analyzing human facial abnormalities, detailed phenotyping, anatomical and molecular atlases, global and specific gene expression patterns, and transcriptional profiling over the course of embryonic and postnatal development in animal models and humans. The integrated data visualization tools, faceted search infrastructure, and curation provided by the FaceBase Hub offer flexible and intuitive ways to interact with these multidisciplinary data. In parallel, the datasets also offer unique opportunities for new collaborations and training for researchers coming into the field of craniofacial studies. Here, we highlight the focus of each spoke project and the integration of datasets contributed by the spokes to facilitate craniofacial research.

Identifying Genetic Sources of Phenotypic Heterogeneity in Orofacial Clefts by Targeted Sequencing

“…We failed to identify significant associations in analyses of coding variants (results not shown), so we hypothesized that functional variants would be regulatory. We examined intervals containing overlapping windows for functional elements based on ENCODE chromatin marks (ENCODE Project Consortium, ; Rosenbloom et al, ) and published craniofacial enhancers (Rada‐Iglesias et al, ; Attanasio et al, ; Brinkley et al, ).…”

Systems biology of facial development: contributions of ectoderm and mesenchyme

“…To understand the ectodermal genetic programs and how they coordinate and integrate with the mesenchymal programs to drive facial development, it is important to obtain a comprehensive understanding of the cellular and molecular changes that occur in each of these tissues during the early stages of facial development. Previous transcriptome studies of human, mouse or chick facial development have provided considerable information concerning gene expression in discrete tissues or regions at specific developmental stages or have generated gene expression profiles of whole prominences over a defined time course (Bhattacherjee et al, 2007; Brinkley et al, 2016; Brugmann et al, 2010; Brunskill et al, 2014; Buchtová et al, 2010; Cai et al, 2005; Ding et al, 2016; Feng et al, 2009; Garaffo et al, 2013; Han et al, 2014; Iwata et al, 2012; Mima et al, 2013; Musselmann et al, 2011; O’Connell et al, 2012; A. S. Potter and S. S. Potter, 2015; Warner et al, 2014).…”

Hunting for genes that shape human faces: Initial successes and challenges for the future

“…Nevertheless, there has been some progress. The FaceBase Consortium, for example, has made available individual‐level genome‐wide variants and 3D facial images on about 6000 individuals of European or African ancestry . As more sharable resources of this kind emerge, these limitations may soon be overcome.…”

“…30 There are other, more basic challenges that we face as a field. While we have made some major advances in phenotyping, the samples we have access to tend to be small, which limits our ability to detect variants with weak phenotypic effects or variants that are rare in the 31 As more sharable resources of this kind emerge, these limitations may soon be overcome.…”