1. FaceBase Resources for Fetal Alcohol Spectrum Disorders Researchers
Steve Scholnick, Ph.D.
NIDCR/NIH

2. What is FaceBase?
Both a consortium working collaboratively on craniofacial development/birth defects and a website ( for disseminating those data to the wider research community
Current focus is on the midface and clefting
Goal is to be a community resource, generating and disseminating large datasets that might be difficult or inefficient for individual labs to generate on their own
developmental stage-specific gene expression profiles, genome-wide genotypes, etc.
tools to search or analyze these data
frees those individual labs from having to generate the data themselves and allows them to more easily generate novel hypotheses

3. FaceBase organization
Coordinating hub
Murray/Marazita (U Iowa, U Pittsburgh)
Clouthier, Artinger, Postlethwait
(U Colorado, U Oregon) miRNAs (zebrafish mouse)
Beaty
(Hopkins)
CNVs/GWAS confirmation (human)
Shapiro
(U Washington) Shape-based image retrieval (human)
Weinberg, Marazita
(U Pittsburgh) 3D Facial Norms database (human)
Spritz
(U Colorado) Genome-wide QTL Morphometry (mouse & human)
Donahue, S. Murray
(Jackson Lab) New conditional clefting models (mouse)
Visel
(LBNL)
ChIP-seq screen for craniofacial enhancers (mouse)
Chai
(USC)
Mutant models/microCT/MRI (mouse)
Potter
(CCHMC)
Gene expression atlas
(mouse)
Fraser
(Caltech/USC) Developmental atlases
(MRI, optical, in situ) (quail & mouse)
Steering Committee
(project PIs)
NIDCR program
Scientific Leadership Group
Animal models
Humans
Both
tools
data

4. FaceBase spoke projects – data types
Project name
Data types
Oral Clefts: Moving from Genome Wide Studies Toward Functional Genomics
Genome-wide CNV scan, DNA sequence data
Research On Functional Genomics, Image Analysis And Rescue Of Cleft Palate
Mouse microCT, gene expression data
Identification of miRNAs involved midfacial development and clefting
miRNA microarray and RNA-seq data
Genetic Tools and Resources for Orofacial Clefting Research
Novel Cre-driver lines
Functional analysis of neural crest & palate: Imaging craniofacial development
microMRI, lightsheet microscopy, ISH
3D Analysis of Facial Variation: Data Repository and Genetics
3D normative facial shape database & GWAS
Global Gene Expression Atlas of Craniofacial Development
Microarray & RNA-seq data across development
Shape-Based Retrieval of 3D Craniofacial Data
Software for image analysis/retrieval & ontology
Genetic Determinants of Orofacial Shape and Relationship to Cleft Lip/Palate
GWAS of normal facial shape in children
Genome-Wide Atlas of Craniofacial Transcriptional Enhancers
ChIP-seq enhancer screen & RNA-seq data

5. Data display/presentation

6. Data available – browse or search

7. Data available – an example

8. Available data formats
A good deal of what’s available on FaceBase consists of global gene expression data .
Depending on the project, data may be available as
Excel spreadsheets
.cel files
That’s great if you’re experienced in global analyses of gene expression and want the raw data
But what about the rest of us?

9. Custom version of UCSC genome browser
Craniofacial tracks: enhancer elements, expression data…
Enhancers and gene expression near mouse Irf6 gene

10. Custom version of UCSC genome browser
Craniofacial tracks: enhancer elements, expression data…
CNVs near human chromosome 7 Hox gene cluster

11. Resource & Tool creation

12. FaceBase mouse repository
PIs: Leah Rae Donahue and Steve Murray at Jackson Lab
A community resource for distributing FaceBase generated strains and useful strains donated by the wider community
maintained at Jackson Labs
many mouse lines
Cre driver strains
mutant models

13. FaceBase mouse repository
Users can follow the progress towards strains of interest on the FaceBase site

14. FaceBase biorepository –human specimens
Run by Jeff Murray’s group at U of Iowa
Cases and related controls
26 different syndromes plus nonsyndromic cases (samples from 590 individuals as of 10/2012)
DNA samples, family histories, environmental exposure records, etc.

15. Other FaceBase resources
Developmental atlases
FishFace (from Chuck Kimmel’s lab),
Ontology of Craniofacial Development and Malformation (OCDM)
Gene Wiki

16. Of particular interest to FASD researcherS…

17. 3D Facial Norms Database
PIs: Seth Weinberg & Mary Marazita, U of Pittsburgh
Goal is to obtain morphometry from males and females years of age (cross-sectional study design)
all normal individuals without family history of craniofacial dysmorphology
All U.S. Caucasians
Recruiting goal of ~3500 individuals. ~1500 recruited as of August, 2012
quantitative morphometric data obtained from facial surface images taken obtained by 3dMD camera system (some caliper measurements as well)
saliva also collected for DNA to be used in future genetic analysis of variation in normal facial shape
Summary data from a subset of subjects are now available online and individual level data can be requested
also available: detailed protocols, pre-computed analyses, Z-score calculator tool for comparison of individual data to norms

18. 3D Facial Norms Database entry page

19. 3D Facial Norms Database summary stats

20. 3D Facial Norms Database summary stats

21. 3D Facial Norms Database search

22. 3D Facial Norms Database results

23. 3D Facial Norms Database Z-score
Z-score calculator for comparing data from an individual to the database
Both Caliper Facial Measurements and 3D Facial Measurements available

24. PI: Rich Spritz, U of Colorado, Denver
Genetic Determinants of Orofacial Shape and Relationship to Cleft Lip/Palate
PI: Rich Spritz, U of Colorado, Denver
Use of the mouse “Collaborative Cross” to identify QTL involved in determining facial shape
Quantitative 3D morphometry of all of the viable CC mouse lines using micro-CT imaging
Both the raw micro-CT data and morphometric data will be available on the FaceBase site.
GWAS of facial shape in humans
3D facial morphometry of Tanzanian children (n >~5700)(all Bantu)
3D mesh images, morphometric data, and genotypes will be available through FaceBase.
Will be incorporated in the 3D Facial Norms database format
Data will be available from smaller numbers of U.S. children of European Caucasian, Hispanic, and Asian backgrounds as well as Masai children from Tanzania
More limited (deidentified) data will also be available through dbGaP

25. Data available – an example

26. Shape-Based Retrieval of 3D Craniofacial Data
PI: Linda Shapiro, U of Washington
“development of computational techniques to represent, quantify, and analyze variants of biological morphology from imaging sources, such as CT scans, MRI scans, and stereo cameras”
For analysis of 3D mesh images:
2D Azimuth-Elevation Histogram
local Features
2D Longitude-Latitude Signature Map
pose Normalization
automatic Cranial Image Generation
Web-based access to these tools using “CranioGUI” java app

27. How do I get data from FaceBase?
Model system and summary human data
Easy! These data are considered “open access”
all you need is an account on the site
request an account on the site at
download data
Individual level human data (genotypes, 3D facial mesh images, etc.)
a little more involved
access controlled by FaceBase Data Access Committee
process described on the “official documents” page
Home page > Resources > Official documents

28. Future developments More data coming
Enhanced data integration and search features
Gene specific pages gathering all FaceBase data about a particular gene + outside links
Dissemination of donated datasets
Planning for the next iteration of the consortium
NIDCR Home  > Grants & Funding  > See Funding Opportunities Sorted by...  > Concept Clearances (Future Research Directions)  > Concept Clearances

29. Questions about FaceBase
At NIDCR
Dr. Steve Scholnick
Contact any of the FaceBase PIs