CCDG: Genetics of Orofacial Clefts and Related Phenotypes

The purpose of this study is to investigate the genetics of orofacial clefts (OFCs) in a large study population, and importantly, to incorporate subclinical phenotypic features into these studies. Orofacial clefts (OFCs) comprise a significant fraction of human birth defects (about 1/700 live births (Rahimov et al. 2012) and represent a major public health challenge, as individuals with these anomalies require surgical, nutritional, dental, speech, medical and behavioral interventions, thus imposing a substantial economic and personal burden (Berk and Marazita 2002*). The most common forms include OFCs of the lip alone (CL, Figure 1A), CL plus cleft palate (CL+CP, Figure 1B) or of the palate only (CP, Figure 1C). Individuals born with OFC may have their first surgical repair at age 3 months, but this initial surgery is just the beginning of a lifetime of health burdens. An individual born with an OFC has a hospital use rate increased for most ages (up to 233% increase for children ages 0-10 years and 16% for middle aged adults (Wehby et al. 2012). Healthcare costs for children with OFCs are estimated to be 800% greater compared with their unaffected peers (Boulet et al. 2009). Data from Denmark show that people born with CL with or without CP (CL/P) have an increased mortality up to age 55, which may be attributed to an increased risk of suicide and/or certain cancers (Christensen et al. 2004). The focus of most OFC genetic research has been CL and/or CP. Furthermore, the majority of OFC, i.e. about 70% of CL/P and 50% of CP is considered "nonsyndromic" (Jones 1988), i.e. isolated anomalies with no other apparent cognitive or structural abnormalities. Figure 1 Sample OFC Types A: Bilateral Cleft Lip; B:Cleft Lip plus Cleft Palate; C:Cleft Palate Alone The factors leading to the majority of nonsyndromic OFCs are still unclear, particularly at an individual family level. As is true for many complex traits, substantial progress in gene identification has occurred in the OFC field in the last two years (Dixon et al. 2011; Marazita 2012). Genome Wide Association Studies (GWAS) and sequencing studies to date by our research team and others have focused on genetic risk factors for overt CL/P and CPO-and have been very successful. A major finding from this work is that OFCs exhibit significant genetic heterogeneity, i.e., multiple genetic regions have been implicated (Beaty et al. 2010; Ludwig et al. 2012). Thus, approaches are needed to understand this genetic heterogeneity. Are there GxG interactions at work? Are there subsets of families, each due to a different gene? Our research group has shown that a promising approach to dissect the etiology of OFC is to focus on subclinical phenotypic features within entire cleft families (not just in affected cases, but also in their non-cleft relatives). These subtle features are believed to represent mild manifestations of the same underlying genetic susceptibility responsible for OFCs; as such, their inclusion in case-control and family-based genetic studies can help to clarify and refine the relationship between genotype and phenotype. The study population comprises a large number of families and individuals (~12,000 individuals) from multiple populations worldwide (Caucasians from the US and Europe, Asians from China and the Philippines, Mixed Native American/Caucasians from South America, and Africans from Nigeria and Ethiopia). There are cases, case families (nuclear families and extended kindreds), as well as controls with no history of OFC nor other developmental defects. *Berk NW, Marazita ML (2002) Costs of Cleft lip and Palate: Personal and Societal Implications. In: Wyszynski DF (ed) Cleft Lip and Palate: From Origin to Treatment. Oxford University Press, Inc., New York, pp 458-467.]]>
OFC Study of Cleft Lip and Palate Demographics and Medical HistoryOFC Study of Cleft Lip and Palate Pregnancy Health HistoryCaliper Measurements: OFC StudyPittsburgh Weighted Values for Speech Symptoms Associated with Velopharyngeal Incompetence - In PersonPittsburgh Weighted Values for Speech Symptoms Associated with Velopharyngeal Incompetence - VideoColombia Screening Form 2003Foreign Sites Cleft Lip and Palate Demographics and Medical HistoryNigeriaCRAN & EthiopiaCRANPREGNANCY, HEREDITY, AND ENVIRONMENT (Puerto Rico)Inclusion criteria for Families with OFCs: Case diagnosed with nonsyndromic OFC (CL/P or CPO). At least 2 additional family members' participation. Male or female, aged 1 month to 110 years. Provide signed and dated informed consent form. Willing to comply with all study procedures and be available for the duration of the study. Inclusion criteria for Controls: Male or female, aged 1 month to 110 years. No known personal or family history of OFCs, genetic conditions, or birth defects. No personal history of facial surgery. In good general health. Provide signed and dated informed consent form. Willing to comply with all study procedures and be available for the duration of the study. Exclusion criteria - individuals who met any of the following criteria were excluded from participation in this study: An affected case with a genetic syndrome or multiple congenital anomalies. An affected case without participation of other family members. Persons who were adopted and cannot report family history. For controls, a positive history of OFC, genetic syndrome/defects in themselves or family. For controls, a previous facial surgery. Male controls may be excluded from certain phenotypes if it is determined that their facial hair hinders the ability to collect accurate facial measurements. ]]>
The current study is the culmination of many years of ongoing collaborations among the study investigators (see investigators section). Molecular genetic studies of orofacial clefts (OFC) by members of this research consortium began in the 1980's, followed by genome-wide linkage studies in the 1990's-early 2000's, and then genome-wide association studies in the 2010's. A rich phenotyping approach was first added to the consortium in 1999 as a project led by Dr. Mary Marazita under a center grant headed by Dr. Jeff Murray. Additional sites were added throughout the 2000's, until multiple populations and a large number of individuals (~12,000) comprise the current study population for genetic studies of OFCs and related phenotypes. All sites completed sample collection and family histories, as well as an array of clinical and subclinical phenotypic assessments. The assessments include questionnaires on Demographic and Medical history, Pregnancy history, facial measurements by caliper and 3D stereophotogrametry, ultrasound of the orbicularis oris muscle, speech assessment for velopharyngeal insufficiency, and lip dermatoglyphics. The caliper exam included a series of standard anthropometric measurements taken on the subject's head using spreading calipers. A 3D facial photo was also acquired and used to generate facial measurement data by using the 3dMD facial camera and software system. High-resolution ultrasound was taken on the upper lip (orbicularis oris muscle) of subjects in an effort to identify subclinical muscular variations that may be informative for orofacial clefting. A one-minute video clip is captured of the ultrasound protocol and saved for later review. Only the participant's Study ID is recorded on the screen so that the reviewer is blinded to the type of subject (case, family member, control). The reviewers assign a score to the video indicating if the muscle is normal or contains a subclinical defect. The protocol begins with the ultrasound in the midline of the lip, and following along the vermilion border moving from the midline to the left side, back to the midline to the right side. The speech assessment consists of a variety of procedures to assess speech patterns and Velopharyngeal Insufficiency (VPI). When feasible, an on-site trained speech pathologist assessed study participants using The Speech and Language Screening form and the Pittsburgh Weighted Values for Speech Symptoms (PWSS) associated with Velopharyngeal Incompetence (VPI Assessment Form). If a trained speech pathologist was not available, lay research staff completed The Speech and Language Screening form and collected speech data by video-taping structured and unstructured speech passages and using a nasometer. The study's speech language pathologist at the University of Pittsburgh analyzed videotapes and nasometer data at a later time and completed the Video VPI Assessment form. Lip photographs were taken of each subject using a digital SLR camera with macro-zoom lens to visualize the lip dermatoglyphics. Three photographs of the complete lower lip, one left side, and one right side photograph were completed. Three photographs of the upper lip of the subject, one left side and one right side were completed. Upper and lower lips were reviewed individually and scored on the presence or absence of lip whorls. Study version 2 makes available additional phenotype data: (1) Information that describes the observed cleft as a non-isolated birth defect or not, based on self-reported structural, neurological, or developmental anomalies, and (2) updated OO (orbicularis oris) muscle phenotype ratings. ]]>