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Center for Craniofacial Innovation

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The Center for Craniofacial Innovation at the Children’s Hospital of Philadelphia is a translational research institute whose stated aim is to advance diagnosis and treatment of craniofacial conditions for children and their families. The Center has four key areas of investigation: 1) functional genomics: identifying key genes and gene variants and their function in craniofacial development, 2) multi-omics: integrating data across genomics, deep phenotyping, biorepository and clinical data to better inform diagnosis and treatment, 3) next generation treatments: advancing treatment with drug screening, gene therapy, biomaterials and devices, and 4) clinical outcomes: establishing best practices in clinical management, technical innovations and patient reported outcomes and initiating first-in-child clinical trials. The center is based on a model of team science, where convergence of scientific, translational, and clinical efforts is used to bridge the clinical gap between fundamental discoveries and pediatric craniofacial care.

Functional Genomics[edit]

Genome sequencing technology continues to advance with ever increasing speed, efficiency and decreased cost. It is now possible to obtain genomic sequencing data in clinical time frame even during the prenatal period[1][2]. However, the exponential and accelerated growth of genomic data has only exacerbated and underscores the difficulty in translating this data to clinically actionable information[3]. For example, whether it is somatic sequencing data from tumors or germline sequencing data from congenital conditions, resolving the sequence information down to a causative gene has for the most part defied computational tools, often requiring experimental evidence to impute pathogenicity[4][5]. Further, newer systems and tools need to be developed to handle the integration and analysis of genomic data.

The functional genomics laboratory at the Center collaborates with human geneticists and data scientists to curate genes associated with congenital craniofacial conditions and interrogate these genes functionally in experimental models[6]. The researchers utilize human iPSC, mouse and zebrafish models to elucidate the function of genes in craniofacial development[7]. Scientists at the center have developed zebrafish, mouse and iPSC cell models and assays that allow functional gene variant testing for IRF6, ESRP1/2, ALX1, and other genes[8][9][10].


The Center considers multi-omics in a broad sense to mean integration of large datasets (genomic sequencing, RNA sequencing, proteomics, deep phenotyping, clinical outcomes) to reveal new insight or actionable information to drive scientific or clinical advances. For craniofacial conditions, the Center is interested in integrating morphometric data, clinical functional data, and molecular diagnosis, as intersection of data across independent approaches increases the significance and robustness of discovery.

Next Generation Treatments[edit]

Advances in gene editing and gene delivery are critical technology enablers of gene therapy applications now revolutionizing medicine and offering hope to patients afflicted with sickle cell disease, leukemia, diabetes, and many other conditions. The Center is developing gene therapy tools to improve treatment of craniofacial conditions.

The Center’s craniofacial surgeons are innovating biomaterials and devices for use in surgical procedures, to replace or enhance bone and soft tissue.

Clinical Outcomes[edit]

CHOP has a robust clinical craniofacial program with broad referrals of high volume and high complexity craniofacial conditions. There is a long-standing history of contribution from CHOP and Penn on treatment of craniosynostosis, cleft lip and palate and other craniofacial conditions. (link) The Center is engaged in many clinical outcome studies to refine surgical procedures, improve safety and patient experience, and initiate first-in-child clinical trials in order to advance care. It works with patient groups to enhance patient advocacy and feedback.


  1. Fan, H. Christina; Gu, Wei; Wang, Jianbin; Blumenfeld, Yair J.; El-Sayed, Yasser Y.; Quake, Stephen R. (July 4, 2012). "Non-invasive prenatal measurement of the fetal genome". Nature. 487 (7407): 320–324. Bibcode:2012Natur.487..320F. doi:10.1038/nature11251. ISSN 1476-4687. PMC 3561905.
  2. Talkowski, Michael E.; Ordulu, Zehra; Pillalamarri, Vamsee; Benson, Carol B.; Blumenthal, Ian; Connolly, Susan; Hanscom, Carrie; Hussain, Naveed; Pereira, Shahrin; Picker, Jonathan; Rosenfeld, Jill A.; Shaffer, Lisa G.; Wilkins-Haug, Louise E.; Gusella, James F.; Morton, Cynthia C. (2012-12-06). "Clinical Diagnosis by Whole-Genome Sequencing of a Prenatal Sample". New England Journal of Medicine. 367 (23): 2226–2232. doi:10.1056/NEJMoa1208594. ISSN 0028-4793. PMC 3579222. PMID 23215558.
  3. Hashiloni‐Dolev, Yael; Nov‐Klaiman, Tamar; Raz, Aviad (June 4, 2019). "Pandora's pregnancy: NIPT, CMA, and genome sequencing—A new era for prenatal genetic testing". Prenatal Diagnosis. 39 (10): 859–865. doi:10.1002/pd.5495. ISSN 0197-3851. Unknown parameter |s2cid= ignored (help)
  4. Yazar, Metin; Özbek, Pemra (2021-01-01). "In Silico Tools and Approaches for the Prediction of Functional and Structural Effects of Single-Nucleotide Polymorphisms on Proteins: An Expert Review". OMICS: A Journal of Integrative Biology. 25 (1): 23–37. doi:10.1089/omi.2020.0141. Unknown parameter |s2cid= ignored (help)
  5. Thusberg, Janita; Olatubosun, Ayodeji; Vihinen, Mauno (January 18, 2011). "Performance of mutation pathogenicity prediction methods on missense variants". Human Mutation. 32 (4): 358–368. doi:10.1002/humu.21445. ISSN 1059-7794. Unknown parameter |s2cid= ignored (help)
  6. Philadelphia, The Children's Hospital of. "Meet Our Craniofacial Program Team". Retrieved 2022-11-01.
  7. "Research | Center For Craniofacial Innovation". CHoP CfCI. Retrieved 2022-11-01.
  8. Carroll, Shannon H.; Macias Trevino, Claudio; Li, Edward B.; Kawasaki, Kenta; Myers, Nikita; Hallett, Shawn A.; Alhazmi, Nora; Cotney, Justin; Carstens, Russ P.; Liao, Eric C. (2020-01-01). "An Irf6 - Esrp1/2 regulatory axis controls midface morphogenesis in vertebrates". Development: dev.194498. doi:10.1242/dev.194498. ISSN 1477-9129.
  9. Li, Edward B.; Truong, Dawn; Hallett, Shawn A.; Mukherjee, Kusumika; Schutte, Brian C.; Liao, Eric C. (2017-09-25). Ekker, Stephen C, ed. "Rapid functional analysis of computationally complex rare human IRF6 gene variants using a novel zebrafish model". PLOS Genetics. 13 (9): e1007009. doi:10.1371/journal.pgen.1007009. ISSN 1553-7404. PMC 5628943. PMID 28945736.
  10. Pini, Jonathan; Kueper, Janina; Hu, Yiyuan David; Kawasaki, Kenta; Yeung, Pan; Tsimbal, Casey; Yoon, Baul; Carmichael, Nikkola; Maas, Richard L; Cotney, Justin; Grinblat, Yevgenya; Liao, Eric C (2020-10-07). "ALX 1‐ related frontonasal dysplasia results from defective neural crest cell development and migration". EMBO Molecular Medicine. 12 (10). doi:10.15252/emmm.202012013. ISSN 1757-4676. PMC 7539331 Check |pmc= value (help). PMID 32914578 Check |pmid= value (help).

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