News & Events

Data releases: Oro Facial Cleft and Oral Health Disparities (28 July 2025)

We are excited to announce new data releases on deep phenotyping of orofacial cleft and discovering oral health disparities in Appalachia:

Oral-Facial Cleft

Oral-Facial Cleft Families: Phenotype and Genetics (OFC1)
Principal Investigators: Mary L. Marazita and Seth Weinberg (University of Pittsburgh)
DOI: https://doi.org/10.25550/5A-FJBJ

Pittsburgh Oral Facial Cleft Studies: Extending the Phenotype of Nonsyndromic Orofacial Clefting (OFC2)
Principal Investigators: Mary L. Marazita and Seth Weinberg (University of Pittsburgh)
DOI: https://doi.org/10.25550/56-ES6P

Description:

Two comprehensive datasets from the University of Pittsburgh project Genetics, Genomics and Deep Phenotyping of Orofacial Clefts are now available on FaceBase. The OFC1 dataset comprises data from 29,369 individuals across 29 global sites, while OFC2 includes 24,754 participants from 6 international locations. Led by Drs. Mary Marazita and Seth Weinberg, these studies aim to identify genetic loci and other etiologic factors associated with nonsyndromic orofacial clefts (OFC), including cleft lip (CL), cleft palate (CP), and CL with or without CP (CL/P). Through deep phenotyping—including 3D facial imaging, dental assessments, intraoral photography, and psychosocial and medical histories—these datasets provide richly detailed profiles of individuals with OFC, their relatives, and unaffected controls. The integration of phenotypic data with genomic analyses (SNP genotyping and whole genome sequencing) enables refined gene-mapping and exploration of broader trait associations.

Oral Health Disparities

COHRA2: Factors Contributing to Oral Health Disparities in Appalachia
Principal Investigators: Mary L. Marazita (University of Pittsburgh), Betsy Foxman (University of Michigan), John R. Shaffer (University of Pittsburgh), Daniel W. McNeil (West Virginia University)
DOI: https://doi.org/10.25550/4Y-4SK4

Related dataset: Center for Oral Health Research in Appalachia, Cohort 1 (COHRA1): a study of northern Appalachian households (Released in 2023)
Principal Investigators: Mary L. Marazita (University of Pittsburgh), Daniel W. McNeil (West Virginia University), John R. Shaffer (University of Pittsburgh), Betsy Foxman (University of Michigan)
DOI: https://doi.org/10.25550/2Q-M86G

Description:

The overarching goal of the Center for Oral Health Research in Appalachia (COHRA2) study is to delineate the covariation between genetic, behavioral, family, and community factors associated with oro-dental disease and tooth loss in rural and urban northern Appalachian families (West Virginia and Pennsylvania). The COHRA2 study investigated factors that contribute to the disparately increased rates of dental caries in children living in Northern Appalachia from birth through age ten years. Specifically, the study focused on the microbiological community that develops in babies before they have teeth, as well as genetic and behavioral/environmental factors of both mothers and babies that predispose children to caries after their teeth erupt. The COHRA2 study was a longitudinal, family-based cohort study with one group with data for 2972 Subjects from 829 households. You can also find the COHRA1 related data set here.

NOTE: All of the above datasets are restricted-access human data. To gain access to this data, you must first go through the process outlined here.

Public Meeting Materials from the 2025 FaceBase Forum (30 June 2025)

The 2025 FaceBase Annual Community Forum, held on June 3 & 4 at the Information Sciences Institute in Marina del Rey, CA, demonstrated the newly emerging capabilities of FaceBase to support not only dental, oral and craniofacial (DOC) research and studies across the translational spectrum, but also in related health domains and systems. We introduced new collaborations with the National Institute of Deafness and Communication Disorders (NIDCD), explored integrating clinical elements into FaceBase with the description of an upcoming pilot, introduced the cutting edge technology of Dynamic MRI, discovered advances in basic DOC research and much, much more. FaceBase also announced their exciting roadmap for the next four years, emphasizing data integration, AI and machine learning applications, and future goals for enhancing research capabilities.

Below you will find comprehensive materials from the one-and-half-days event.

• Bios of Speakers and Panelists

Slides and Webcasts from Presentations and Panels

Poster Session Presenters

All our thanks go to those esteems speakers and panelists and to all who joined us! Looking forward to seeing you at next year’s Forum!

Data release: SHH expression in the Frontonasal Ectodermal Zone (21 May 2025)

We are excited to announce a new data release from a PLOS Genetics paper on SHH expression in the Frontonasal Ectodermal Zone that depicts a new enhancer element!

PBX1 and PBX3 transcription factors regulate SHH expression in the Frontonasal Ectodermal Zone through complementary mechanisms Principal Investigators: Licia Selleri and Ralph S. Marcucio (University of California, San Francisco)

Citation: 

Mok CH, Hu D, Losa M, Risolino M, Selleri L, Marcucio RS (2025) PBX1 and PBX3 transcription factors regulate SHH expression in the Frontonasal Ectodermal Zone through complementary mechanisms. PLoS Genet 21(5): e1011315. https://doi.org/10.1371/journal.pgen.1011315

FaceBase Dataset:

• ATAC-seq and ChIP-seq targeting PBX1 and PBX3 in the normal chick FEZ at HH22 (https://doi.org/10.25550/5G-BBG8)

Description:

Facial development is orchestrated by complex molecular interactions among signaling molecules and transcription factors, a class of proteins that regulate gene expression. Disruption of these interactions can lead to congenital facial malformations, affecting the lives of patients and their families. Understanding the molecular basis of these interactions during embryonic facial development will provide key insights into the origin of these disorders and may ultimately provide novel therapeutic targets. SHH is one of the key genes encoding a signaling molecule that regulates facial development. During early embryonic development, SHH is expressed in a signaling center in the surface cell layer that covers part of the face. This signaling center regulates proliferation to control proper outgrowth of the upper jaw. In the present study, we demonstrated that PBX1 and PBX3 transcription factors control expression of SHH at the molecular level. We identified a DNA element, SFE1, located in a regulatory region of the SHH locus. SFE1 induces SHH transcription when associated with PBX1 and represses transcription when associated with PBX3. These findings highlight the intricate molecular mechanisms underlying regulation of SHH expression and advance current knowledge of the regulatory pathways that control midfacial development.

This figure was generated from the ChIP-seq and ATAC-seq data in this study, submitted to FaceBase, and it shows the location of SFE1, a new enhancer element that we identified from this study.

Data release: TGF-β Signaling and Craniofacial Morphogenesis (20 May 2025)

We are excited to announce new data releases from a Nature Communications paper on TGF-β Signaling and Craniofacial Morphogenesis featuring high resolution spatial genomics data!

High-resolution spatial transcriptomics and cell lineage analysis reveal spatiotemporal cell fate determination during craniofacial development (2 datasets) Principal Investigator: Yang Chai (University of Southern California)

Citation: 

Feng, Jifan & Janeckova, Eva & Guo, Tingwei & Ziaei, Heliya & Zhang, Mingyi & Geng, Jessica & Cha, Sa & Araujo-Villalba, Angelita & Liu, Mengmeng & Ho, Thach-Vu & Chai, Yang. (2025). High-resolution spatial transcriptomics and cell lineage analysis reveal spatiotemporal cell fate determination during craniofacial development. Nature Communications. 16. 10.1038/s41467-025-59206-2. 

The authors employed scRNA-seq analysis alongside a seqFISH-based spatial genomics approach for high-resolution visualization of spatially resolved gene expression profiles for the developing palate and other craniofacial regions in the mouse embryos. The raw and processed scRNA-seq data from embryonic palatal tissue at different developmental stages (E12.5, E13.5, E14.5, E15.5, and E18.5) generated in this study has been deposited in FaceBase under the DOI 10.25550/62-QZ1A. The raw and processed sequencing-FISH data for anterior and posterior embryonic heads at E12.5, E13.5, and E15.5 are available in the FaceBase database under the DOI 10.25550/62-Y0VT.

FaceBase Achieves CoreTrustSeal Certification (26 March 2025)

FaceBase has officially been awarded the CoreTrustSeal certification. This recognition affirms our commitment to maintaining a trusted, sustainable, and FAIR (Findable, Accessible, Interoperable, Reusable) data repository for the dental, oral, and craniofacial research community.

The CoreTrustSeal is an internationally recognized certification that evaluates data repositories based on 16 rigorous requirements related to sustainability, data integrity, and long-term accessibility.

This milestone reflects our ongoing efforts to support open science, facilitate data sharing, and enhance research reproducibility.

To learn more about the CoreTrustSeal certification and what it means for FaceBase, visit CoreTrustSeal or read our CoreTrustSeal application.