Six NSCL/P loci show associations with normal-range craniofacial variation

Objectives: Orofacial clefting is one of the most prevalent craniofacial malformations. Previous research has demonstrated that unaffected relatives of patients with non-syndromic cleft lip with/without cleft palate (NSCL/P) show distinctive facial features, which can be an expression of underlying NSCL/P susceptibility genes. These results support the hypothesis that genes involved in the occurrence of a cleft also play a role in normal craniofacial development. In this study, we investigated the influence of genetic variants associated with NSCL/P on normal-range variation in facial shape. Methods: A literature review of genome wide association studies (GWAS) investigating the genetic etiology of NSCL/P was performed, resulting in a list of 75 single nucleotide polymorphisms (SNPs) located in 38 genetic loci. Genotype data were available for 65 of these selected SNPs in three datasets with a combined sample size of 7,418 participants of European ancestry, whose 3D facial images were also available. The effect of each SNP was tested using a multivariate canonical correlation analysis (CCA) against 63 hierarchically-constructed facial segments in each of the three datasets and meta-analyzed. This allowed for the investigation of associations between SNPs known to be involved in NSCL/P and normal-range facial shape variations in a global-to-local perspective, without preselecting specific facial shape features or characteristics. Results: Six NSCL/P SNPs showed significant associations with variation in normal-range facial morphology. rs6740960 showed significant effects in the chin area (p = 3.71 × 10−28). This SNP lies in a non-coding area. Another SNP, rs227731 near the NOG gene, showed a significant effect in the philtrum area (p = 1.96 × 10−16). Three SNPs showed significant effects on the shape of the nose. rs742071 (p = 8.71 × 10−14), rs34246903 (p = 6.87 × 10−12), and rs10512248 (p = 8.4 × 10−9). Respectively, these SNPs are annotated to PAX7, MSX1, and PTCH1. Finally, rs7590268, an intron variant of THADA, showed an effect in the shape of the supraorbital ridge (p = 3.84 × 10−7). Conclusions: This study provides additional evidence NSCL/P-associated genetic variants influence normal-range craniofacial morphology, with significant effects observed for the chin, the nose, the supraorbital ridges and the philtrum area

SNPs associated with testosterone levels influence human facial morphology

Many factors influence human facial morphology, including genetics, age, nutrition, biomechanical forces, and endocrine factors. Moreover, facial features clearly differ between males and females, and these differences are driven primarily by the influence of sex hormones during growth and development. Specific genetic variants are known to influence circulating sex hormone levels in humans, which we hypothesize, in turn, affect facial features. In this study, we investigated the effects of testosterone-related genetic variants on facial morphology. We tested 32 genetic variants across 22 candidate genes related to levels of testosterone, sex hormone-binding globulin (SHGB) and dehydroepiandrosterone sulfate (DHEAS) in three cohorts of healthy individuals for which 3D facial surface images were available (Pittsburgh 3DFN, Penn State and ALSPAC cohorts; total n = 7418). Facial shape was described using a recently developed extension of the dense-surface correspondence approach, in which the 3D facial surface was partitioned into a set of 63 hierarchically organized modules. Each variant was tested against each of the facial surface modules in a multivariate genetic association-testing framework and meta-analyzed. Additionally, the association between these candidate SNPs and five facial ratios was investigated in the Pittsburgh 3DFN cohort. Two significant associations involving intronic variants of SHBG were found: both rs12150660 (p = 1.07E-07) and rs1799941 (p = 6.15E-06) showed an effect on mandible shape. Rs8023580 (an intronic variant of NR2F2-AS1) showed an association with the total and upper facial width to height ratios (p = 9.61E-04 and p = 7.35E-04, respectively). These results indicate that testosterone-related genetic variants affect normal-range facial morphology, and in particular, facial features known to exhibit strong sexual dimorphism in humans

Six NSCL/P Loci Show Associations With Normal-Range Craniofacial Variation

Objectives: Orofacial clefting is one of the most prevalent craniofacial malformations. Previous research has demonstrated that unaffected relatives of patients with non-syndromic cleft lip with/without cleft palate (NSCL/P) show distinctive facial features, which can be an expression of underlying NSCL/P susceptibility genes. These results support the hypothesis that genes involved in the occurrence of a cleft also play a role in normal craniofacial development. In this study, we investigated the influence of genetic variants associated with NSCL/P on normal-range variation in facial shape.Methods: A literature review of genome wide association studies (GWAS) investigating the genetic etiology of NSCL/P was performed, resulting in a list of 75 single nucleotide polymorphisms (SNPs) located in 38 genetic loci. Genotype data were available for 65 of these selected SNPs in three datasets with a combined sample size of 7,418 participants of European ancestry, whose 3D facial images were also available. The effect of each SNP was tested using a multivariate canonical correlation analysis (CCA) against 63 hierarchically-constructed facial segments in each of the three datasets and meta-analyzed. This allowed for the investigation of associations between SNPs known to be involved in NSCL/P and normal-range facial shape variations in a global-to-local perspective, without preselecting specific facial shape features or characteristics.Results: Six NSCL/P SNPs showed significant associations with variation in normal-range facial morphology. rs6740960 showed significant effects in the chin area (p = 3.71 × 10−28). This SNP lies in a non-coding area. Another SNP, rs227731 near the NOG gene, showed a significant effect in the philtrum area (p = 1.96 × 10−16). Three SNPs showed significant effects on the shape of the nose. rs742071 (p = 8.71 × 10−14), rs34246903 (p = 6.87 × 10−12), and rs10512248 (p = 8.4 × 10−9). Respectively, these SNPs are annotated to PAX7, MSX1, and PTCH1. Finally, rs7590268, an intron variant of THADA, showed an effect in the shape of the supraorbital ridge (p = 3.84 × 10−7).Conclusions: This study provides additional evidence NSCL/P-associated genetic variants influence normal-range craniofacial morphology, with significant effects observed for the chin, the nose, the supraorbital ridges and the philtrum area

Gezichtsmorfologie geassocieerd met schisis: een studie gebaseerd op geavanceerde 3D morfometrie

Cleft lip with/without cleft palate (CL/P) is one of the most common congenital facial anomalies with an incidence of approximately 1 in 700 births. Orofacial clefts can be responsible for a major social and psychological burden in the lives of the patients and their families. These patients require a long and multidisciplinary follow-up until adulthood, including several surgical procedures, speech therapy, orthodontics, genetic counseling and psychological assistance. CL/P can be associated with other birth defects in the context of a syndrome, but in the majority of cases (70%), they are an isolated finding. The heterogeneous orofacial cleft group can be subdivided in two classes: CL/P and isolated cleft palate (CP), based on differences in prevalence and embryological etiology. Non-syndromic cleft lip with/without cleft palate (NSCL/P) is a complex condition, meaning that the phenotype is not caused by one gene. Instead, a combination of multiple genes and environmental factors are responsible for the etiology of NSCL/P. This complex etiology causes the heterogeneous phenotype in complex conditions and contributing etiologic factors are difficult to identify. Although tremendous advancements were obtained in the knowledge about etiology of NSCL/P, it remains important to find new approaches to fully unravel the genetic etiology of NSCL/P. Therefore, more accurate phenotyping is vital before doing linkage or association studies. It is possible that certain subphenotypes or endophenotypes are present in unaffected family members of patients with NSCL/P. When doing a linkage analysis or association study, it is essential to take these endophenotypes into account. Relatives showing subphenotypes or endophenotypes cannot be considered to be fully ‘unaffected’. Further, accurate phenotyping of syndromic and non-syndromic patients with orofacial clefts can be helpful to delineate more homogeneous subgroups in this diverse patient population. Facial phenotyping has evolved from direct anthropometry (measuring the face by physical contact with the subject) to indirect anthropometry on images of the face. Indirect measurements were originally conducted on 2D pictures, but a face is intrinsically a 3D object, so the implementation of 3D facial imaging was a logical evolution. 3D scanning preserves the 3D nature of the face and pose variations can be corrected by rotating and translating the images, so the face can be seen from every possible viewpoint. The main advantage of using images is that these can be collected for repeatable measurements, allowing calculation of inter-rater variability and future analysis. Besides the advancement of acquisition techniques to capture facial morphology, the analytic methods to describe facial shape must also gain in resolution, precision, and power. Facial shape is often still described using only a sparse set of specific biological landmarks, which are indicated manually on each facial shape. Several extensions to spatially-dense landmarks have been proposed, including quasi-landmarks (mesh-based representation across the whole surface) and semi-landmarks (landmarks relative to other landmarks). For instance, the anthropometric mask has been proposed recently to expand the classic or true landmarks to 10000 spatially-dense quasi-landmarks. The main advantage of a spatially-denser set of landmarks is that they provide more coverage and therefore a fuller description of shapes. A statistical shape analysis can always be performed to represent the typical variability between similarly shaped objects. Shape regression for example, is a useful technique to investigate the effect of an independent variable of interest on facial morphology. In this dissertation, the focus lies on the description of facial morphology in families with a history of syndromic and non-syndromic orofacial clefting. Ultimately, the goal of this scientific work is to gain insight in the interaction between phenotype and genotype in one of the most frequent congenital conditions: orofacial clefting. The investigation of endophenotypes (phenotypic features associated with a condition without being a deviaton from the standard, and considered to be an expression of underlying susceptibility genes) is a valuable approach to gain more insight in the etiology of NSCL/P. The concept of endophenotypes is not new in research on the etiology of orofacial clefts. Most studies on endophenotypes in this field have focused on subtle variations in facial morphology of unaffected relatives. Furthermore, differences between relatives of NSCL/P patients and controls have been observed in the anatomy of the orbicularis oris muscle, nasolabial fold continuity, and occurrence of lip whorls. Our research identified a broadening of the upper facial area and midfacial retrusion as facial characteristics in a diverse group of unaffected relatives of patients with NSCL/P. Patients with NSCL/P and their unaffected relatives also showed reduced olfactory function in comparison with a control group, which was associated differences in the central olfactory structures (olfactory bulb and sulcus). Relatives with a diminished smell capacity also showed a smaller upper nasal area, compared to relatives with a normal smell capacity. There is thus a variation in facial morphology in different subgroups of unaffected relatives. This suggests that the biological pathway resulting in a fusion deficit of the facial prominences in their offspring is different. Different susceptibility genes may increase the chance of non-fusion of the maxillary and medial nasal prominences during embryogenesis via different biological pathways. Second, facial morphology is objectively described in patients with an isolated CP or Pierre Robin Sequence (PRS) and compared with a matched unaffected control group, using 3D facial morphometrics. Further, differences in facial morphology between patients with isolated CP and patients diagnosed with PRS are investigated. Our results show that both patient groups show retrusion of the chin, and this effect was more pronounced in the patients with PRS. On top of this effect, patients with PRS show additional facial characteristics and significantly more tooth agenesis. In this study, we showed that 3D facial imaging and morphometrics is an excellent tool to differentiate between two very similar phenotypes, such as CP and PRS. Although classically used for this type of analysis, this differentiation was not possible based on cephalometric analysis. One of the most common microdeletion syndromes, associated with cleft palate, is 22q11.2 deletion syndrome (22q11.2DS). We investigated the 3D facial morphology of patients with an atypical 22q11.2 deletion and linked it to its underlying genetic etiology. Our observations show that haploinsufficiency of TBX1 is not sufficient to cause facial dysmorphology associated with 22q11.2DS, in contradiction to the general belief. CRKL however is a good candidate gene. We conclude that advanced 3D morphometrics, as used in the described studies, is an excellent method to accurately describe and objectively compare facial morphology associated with orofacial clefting. This is a first step in the investigation of the correlation between facial morphology associated with orofacial clefting and underlying susceptibility genes. By setting-up large, international and multidisciplinary collaborations, we are convinced that this approach can lead to a better insight in the phenotype-genotype interaction in orofacial clefting.Roosenboom J., ''Facial morphology associated with orofacial clefting. A study using advanced 3D morphometrics'', Proefschrift voorgedragen tot het behalen van het doctoraat in de biomedische wetenschappen, KU Leuven, June 2016, Leuven, Belgium.nrpages: 141status: publishe

Smell deficits as an endophenotype in patients with nonsyndromic cleft lip and/or palate and their non-affected first-degree relatives: a pilot study

Roosenboom J., Claes P., Hens G., ''Smell deficits as an endophenotype in patients with nonsyndromic cleft lip and/or palate and their non-affected first-degree relatives: a pilot study'', Abstractbook 24th international conference of European Chemoreception Research Organization - ECRO 2014, pp. 229, September 10-13, 2014, Dijon, France.status: publishe

Facial characteristics and olfactory dysfunction: two endophenotypes related to non-syndromic cleft lip and/or palate

Roosenboom J., Saey I., Peeters H., Devriendt K., Claes P., Hens G., ''Facial characteristics and olfactory dysfunction: two endophenotypes related to non-syndromic cleft lip and/or palate'', Craniofacial Society of Great Britain and Ireland annual scientific conference, April 15-17, 2015, London, UK, 2015.status: publishe

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

There is ample evidence from heritability studies, genetic syndromes and experimental animal models that facial morphology is strongly influenced by genes. In this brief review, we present an up-to-date overview of the efforts to identify genes associated with the size and shape of human facial features. We discuss recent methodological advances that have led to breakthroughs, but also the multitude of challenges facing the field. We offer perspective on possible applications of this line of research, particularly in the context of the precision genomics movement.status: publishe

Exploring the underlying genetics of craniofacial morphology through various sources of knowledge

The craniofacial complex is the billboard of sorts containing information about sex, health, ancestry, kinship, genes, and environment. A thorough knowledge of the genes underlying craniofacial morphology is fundamental to understanding craniofacial biology and evolution. These genes can also provide an important foundation for practical efforts like predicting faces from DNA and phenotype-based facial diagnostics. In this work, we focus on the various sources of knowledge regarding the genes that affect patterns of craniofacial development. Although tremendous successes recently have been made using these sources in both methodology and biology, many challenges remain. Primary among these are precise phenotyping techniques and efficient modeling methods.Roosenboom J., Hens G., Mattern B.C., Shriver M.D., Claes P., ''Exploring the underlying genetics of craniofacial morphology through various sources of knowledge'', BioMed research international, vol. Article ID 3054578, 9 pp., 2016.status: publishe

A comprehensive orthodontic diagnosis in children with 22Q11.0 deletion syndrime

AIM: 22q11.2 deletion syndrome (DS) is one of the most frequent microdeletion syndromes and presents with a highly variable and extensive phenotype. Facial features associated with this syndrome can however be very subtle and are not often objectively described. In order to construct a comprehensive orthodontic diagnosis, the craniofacial and dental characteristics of children with 22q11.2 DS were investigated. MATERIALS AND METHOD: Clinical photographs, a panoramic and a cephalometric radiograph, dental casts and a three-dimensional (3D) facial surface scan of 20 children of west-European descent with a confirmed diagnosis of 22q11.2 DS were prospectively collected. 3D scans were compared to scans of a matched control group and analyzed using a spatially-dense analysis approach. Cephalometric radiographs were digitally traced and measurements were compared with normal values. Occlusal and dental features were studied on dental casts and panoramic radiographs. RESULTS: 3D facial analysis showed a significant retrusion of the lower part of the face in children with 22q11.2 DS. Tracing of the cephalometric radiographs revealed that the skeletal relationship between the upper and lower jaw was a mild distal relationship and the cranial base angle was slightly enlarged. Measurements for molar occlusion, overjet and overbite did not differ significantly from normal values. Four patients presented with dental agenesis and one had a double tooth transposition. CONCLUSIONS: The most important craniofacial and dental features found for this study group are a significant retrusion of the lower part of the face and an augmented prevalence of tooth agenesis.status: publishe

Haploinsufficiency of TBX1 is not responsible for facial dysmorphology in patients with 22q11.2 deletion syndrome

Roosenboom J., Demaerel W., Breuls M., Appermont E., Claes P., Hammond P., Peeters H., Devriendt K., Hens G., ''Haploinsufficiency of TBX1 is not responsible for facial dysmorphology in patients with 22q11.2 deletion syndrome'', Abstract book 10th biennial international 22q11.2 conference, pp. 56, July 20-22, 2016, Sirmione, Italy.status: publishe