A LINE-1 insertion in DLX6 is responsible for cleft palate and mandibular abnormalities in a canine model of Pierre Robin sequence

Targeting transposable elements in cancer: developments and opportunities

Transposable elements (TEs), comprising nearly 50% of the human genome, have transitioned from being perceived as "genomic junk" to key players in cancer progression. Contemporary research links TE regulatory disruptions with cancer development, underscoring their therapeutic potential. Advances in long-read sequencing, computational analytics, single-cell sequencing, proteomics, and CRISPR-Cas9 technologies have enriched our understanding of TEs' clinical implications, notably their impact on genome architecture, gene regulation, and evolutionary processes. In cancer, TEs, including long interspersed element-1 (LINE-1), Alus, and long terminal repeat (LTR) elements, demonstrate altered patterns, influencing both tumorigenic and tumor-suppressive mechanisms. TE-derived nucleic acids and tumor antigens play critical roles in tumor immunity, bridging innate and adaptive responses. Given their central role in oncology, TE-targeted therapies, particularly through reverse transcriptase inhibitors and epigenetic modulators, represent a novel avenue in cancer treatment. Combining these TE-focused strategies with existing chemotherapy or immunotherapy regimens could enhance efficacy and offer a new dimension in cancer treatment. This review delves into recent TE detection advancements, explores their multifaceted roles in tumorigenesis and immune regulation, discusses emerging diagnostic and therapeutic approaches centered on TEs, and anticipates future directions in cancer research.

A naturally occurring canine model of syndromic congenital microphthalmia

In humans, the prevalence of congenital microphthalmia is estimated to be 0.2-3.0 for every 10,000 individuals, with nonocular involvement reported in ∼80% of cases. Inherited eye diseases have been widely and descriptively characterized in dogs, and canine models of ocular diseases have played an essential role in unraveling the pathophysiology and development of new therapies. A naturally occurring canine model of a syndromic disorder characterized by microphthalmia was discovered in the Portuguese water dog. As nonocular findings included tooth enamel malformations, stunted growth, anemia, and thrombocytopenia, we hence termed this disorder Canine Congenital Microphthalmos with Hematopoietic Defects. Genome-wide association study and homozygosity mapping detected a 2 Mb candidate region on canine chromosome 4. Whole-genome sequencing and mapping against the Canfam4 reference revealed a Short interspersed element insertion in exon 2 of the DNAJC1 gene (g.74,274,883ins[T70]TGCTGCTTGGATT). Subsequent real-time PCR-based mass genotyping of a larger Portuguese water dog population found that the homozygous mutant genotype was perfectly associated with the Canine Congenital Microphthalmos with Hematopoietic Defects phenotype. Biallelic variants in DNAJC21 are mostly found to be associated with bone marrow failure syndrome type 3, with a phenotype that has a certain degree of overlap with Fanconi anemia, dyskeratosis congenita, Shwachman-Diamond syndrome, Diamond-Blackfan anemia, and reports of individuals showing thrombocytopenia, microdontia, and microphthalmia. We, therefore, propose Canine Congenital Microphthalmos with Hematopoietic Defects as a naturally occurring model for DNAJC21-associated syndromes.

The most common congenital malformations in dogs: Literature review and practical guide

Congenital malformations can affect almost 7% of canine newborns. The increase of commercial dog breeding and inbreeding used to maintain the striking characteristics of each breed, the appearance of malformations has become increasingly common, especially in brachycephalic dogs. The causes are diverse, and include genetic, nutritional, iatrogenic, and infectious factors, often making it difficult to establish a cause-consequence relationship. The high mortality associated with malformations comes not only from the fact that some are incompatible with life, but also because even if many undergo surgical treatment or correction, they require specific management, monitoring, and clinical treatment for an indefinite period of time. The most common malformations such as cleft lip and palate, hydrocephalus and anasarca have been studied for a long time, and it is currently known that brachycephalic dogs have a greater predisposition, however, for other less common conditions as gastroschisis and hypospadias, there is only a few case reports. The appearance of congenital defects in a litter leads to financial losses for the breeder, emotional losses for the owner and the veterinarian and harms the well-being of that individual. For this reason, the aim of this review article is to gather relevant information on the characteristics, diagnosis, and management of the main malformations in puppies. It is essential that the veterinarian is prepared to diagnose and treat these conditions, reducing negative impacts on animals and owners.

Cleft Lip and Palate in Four Full-Sib Puppies from a Single Litter of Staffordshire Bull Terrier Dogs: An Anatomical and Genetic Study

Cleft lip and palate (CLP) is a well-known congenital defect in dogs, characterized by abnormal communication between the oral and nasal cavities. Its incidence rate is high and affects all dog breeds. The etiology of CLP is thought to be multifactorial, caused by both genetic and environmental factors. In this study, four puppies out of seven from a single litter of Staffordshire Bull Terrier dogs with craniofacial abnormalities were anatomically and genetically examined. Classical anatomical preparation, dyed-latex-injection of the arterial vessels, and cone-beam computed tomography were used. The puppies showed variations in their observable abnormalities: three of them had a complete cleft of the palate on both sides, while one puppy had a cleft on the right side only. Cytogenetic analysis showed a normal diploid chromosome number (2n = 78,XX or 78,XY) in the studied animals. Known genomic variants of CLP were examined in the ADAMTS20, DLX6, and MYH3 genes, but no mutations were identified. Further studies are needed to identify the breed-specific genetic variants associated with canine CLP.

DLX6 and MSX1 from saliva samples as potential predictors of mandibular size: A cross-sectional study

INTRODUCTION

Morphologic features of the mandible are influenced by the genes of each individual. Mandible size is important to orthodontists because the mandible is the mechanism by which the lower face influences facial esthetics and dental function. To date, no biological marker has been identified that indicates eventual mandible size. This study aimed to correlate the expression of DLX5, DLX6, EDN1, HAND2, PRRX1, and MSX1 to mandible size.

METHODS

Fifty-nine orthodontic patients aged >6 years who had available cephalometric radiographs were studied. Patients were classified on the basis of condylion-to-gnathion measurements. Messenger RNA was isolated from saliva and subjected to real-time quantitative polymerase chain reaction.

RESULTS

Threshold cycle values for subjects with small mandibles (>1 standard deviation [SD] from the mean) had the least expression of DLX6 and MSX1. Threshold cycle values for subjects with large mandibles (>1 SD) had less expression of DLX6 and MSX1 than subjects within 1 SD but more than those with small mandibles.

CONCLUSIONS

DLX6 and MSX1 are related to mandible development and size. This finding could be used to improve treatment planning for medical and dental professionals seeking to understand the impact of genetics on bone growth.

Identification of Genetic Risk Factors for Monogenic and Complex Canine Diseases

Advances in DNA sequencing and other technologies have greatly facilitated the identification of genetic risk factors for inherited diseases in dogs. We review recent technological developments based on selected examples from canine disease genetics. The identification of disease-causing variants in dogs with monogenic diseases may become a widely employed diagnostic approach in clinical veterinary medicine in the not-too-distant future. Diseases with complex modes of inheritance continue to pose challenges to researchers but have also become much more tangible than in the past. In addition to strategies for identifying genetic risk factors, we provide some thoughts on the interpretation of sequence variants that are largely inspired by developments in human clinical genetics.

Chloroquine regulates the proliferation and apoptosis of palate development on mice embryo by activating P53 through blocking autophagy in vitro

Cleft lip and palate is one of the most frequent congenital developmental defects. Autophagy is a highly conserved process of cell self-degradation in eukaryotes, involving multiple biological processes in which chloroquine (CQ) is the most common inhibitor. However, whether CQ affects and how it affects palate development is unknown. Mouse embryonic palatal cells (MEPCs) were treated with CQ to observe cell viability, apoptosis, migration, osteogenic differentiation by cell proliferation assay, flow cytometric analysis, scratch assay, and alizarin red staining. PI staining was used to measure cell cycle distribution. Immunofluorescence (IF) assay and transmission electron microscopy were used to detect autophagosomes. The autophagy-related factors (LC3 and P62), apoptosis-related markers (P53, caspase-3 cleaved caspase-3, BAX, and BCL-2), and cell cycle-related proteins (P21, CDK2, CDK4, cyclin D1, and cyclin E) were all measured by western blot. CQ inhibited the proliferation of MEPCs by arresting the G0/G1 phase of the cell cycle in a concentration- and time-dependent manner with cell cycle-related proteins P21 upregulated and CDK2, CDK4, cyclin D1, and cyclin E downregulated. Then we detected CQ also induced cell apoptosis in a dose-dependent manner by decreasing the BCL-2/BAX ratio and increasing cleaved caspase-3. Next, it was investigated that migration and osteogenesis of MEPCs decreased with CQ treatment in a dose-dependent manner. Meanwhile, CQ blocked the autophagy pathway by upregulating LC3II and P62 expressions which activated the P53 pathway. CQ activates P53 which affects MEPC biological characteristics by changing the proliferation and apoptosis of MEPCs through inhibiting autophagy.

Brachygnathia Inferior in Cloned Dogs Is Possibly Correlated with Variants of Wnt Signaling Pathway Initiators

Abnormalities in animals cloned via somatic cell nuclear transfer (SCNT) have been reported. In this study, to produce bomb-sniffing dogs, we successfully cloned four healthy dogs through SCNT using the same donor genome from the skin of a male German shepherd old dog. Veterinary diagnosis (X-ray/3D-CT imaging) revealed that two cloned dogs showed normal phenotypes, whereas the others showed abnormal shortening of the mandible (brachygnathia inferior) at 1 month after birth, even though they were cloned under the same conditions except for the oocyte source. Therefore, we aimed to determine the genetic cause of brachygnathia inferior in these cloned dogs. To determine the genetic defects related to brachygnathia inferior, we performed karyotyping and whole-genome sequencing (WGS) for identifying small genetic alterations in the genome, such as single-nucleotide variations or frameshifts. There were no chromosomal numerical abnormalities in all cloned dogs. However, WGS analysis revealed variants of Wnt signaling pathway initiators (WNT5B, DVL2, DACT1, ARRB2, FZD 4/8) and cadherin (CDH11, CDH1like) in cloned dogs with brachygnathia inferior. In conclusion, this study proposes that brachygnathia inferior in cloned dogs may be associated with variants in initiators and/or regulators of the Wnt/cadherin signaling pathway.

Long-read assembly of a Great Dane genome highlights the contribution of GC-rich sequence and mobile elements to canine genomes

Technological advances have allowed improvements in genome reference sequence assemblies. Here, we combined long- and short-read sequence resources to assemble the genome of a female Great Dane dog. This assembly has improved continuity compared to the existing Boxer-derived (CanFam3.1) reference genome. Annotation of the Great Dane assembly identified 22,182 protein-coding gene models and 7,049 long noncoding RNAs, including 49 protein-coding genes not present in the CanFam3.1 reference. The Great Dane assembly spans the majority of sequence gaps in the CanFam3.1 reference and illustrates that 2,151 gaps overlap the transcription start site of a predicted protein-coding gene. Moreover, a subset of the resolved gaps, which have an 80.95% median GC content, localize to transcription start sites and recombination hotspots more often than expected by chance, suggesting the stable canine recombinational landscape has shaped genome architecture. Alignment of the Great Dane and CanFam3.1 assemblies identified 16,834 deletions and 15,621 insertions, as well as 2,665 deletions and 3,493 insertions located on secondary contigs. These structural variants are dominated by retrotransposon insertion/deletion polymorphisms and include 16,221 dimorphic canine short interspersed elements (SINECs) and 1,121 dimorphic long interspersed element-1 sequences (LINE-1_Cfs). Analysis of sequences flanking the 3' end of LINE-1_Cfs (i.e., LINE-1_Cf 3'-transductions) suggests multiple retrotransposition-competent LINE-1_Cfs segregate among dog populations. Consistent with this conclusion, we demonstrate that a canine LINE-1_Cf element with intact open reading frames can retrotranspose its own RNA and that of a SINEC_Cf consensus sequence in cultured human cells, implicating ongoing retrotransposon activity as a driver of canine genetic variation.

Expression of DLX6 Gene in Mandibular Deficiency (Retrognathic Mandible): A Randomized Clinical and Genetic Study

Introduction

There are various genes that affect craniofacial development and among the important genes that affect jaw development is distal-less homeobox (DLX) 6 genes. The present study was carried out to determine the role of DLX6 gene variations in mandibular deficiency.

Methods

Thirty subjects having retrognathic mandible were evaluated by clinical examination and assessed using lateral cephalometric radiographs based on cephalometrics for orthognathic surgery (COGS) analysis of hard tissue with N-Pog parameters being less than -13 mm. For the same subjects, saliva samples were taken and sent to biotechnology labs for genetic evaluation. DNA was isolated from salivary samples using a DNA extraction kit and was subjected to polymerase chain reaction (PCR) amplification and sequencing. Single nucleotide polymorphisms (SNP) analysis was done to assess the role of DLX6 gene in these study subjects.

 Results

 All 30 subjects showed N-POG parameters of COGS analysis for hard tissue to be less than -13mm, confirming retrognathic mandible. SNP analysis of subjects showed no SNPs in any EXON of the DLX6 gene for all 30 study samples.

Conclusion

 No variations in DLX6 gene were found in the present study. Further studies are required to investigate other genes that could be involved in the cause of retrognathic mandible with a larger sample size and to include subjects in the sample having features other than mandibular retrognathia like hearing loss, abnormal pinnae, ectrodactyly, cleft palate, developmental delay and abnormal teeth to determine the contribution of DLX6 gene variations in mandibular deficiency. 

Phenotypes, Developmental Basis, and Genetics of Pierre Robin Complex

The phenotype currently accepted as Pierre Robin syndrome/sequence/anomalad/complex (PR) is characterized by mandibular dysmorphology, glossoptosis, respiratory obstruction, and in some cases, cleft palate. A causative sequence of developmental events is hypothesized for PR, but few clear causal relationships between discovered genetic variants, dysregulated gene expression, precise cellular processes, pathogenesis, and PR-associated anomalies are documented. This review presents the current understanding of PR phenotypes, the proposed pathogenetic processes underlying them, select genes associated with PR, and available animal models that could be used to better understand the genetic basis and phenotypic variation of PR.

DLX6 promotes cell proliferation and survival in oral squamous cell carcinoma

OBJECTIVE

Distal-less homeobox 6 (DLX6) has been reported to play important roles in the development of craniofacial structures, inner ear, limb, and brain. We found in our previous investigation that DLX6 was significantly highly expressed in oral cancer tissues in The Cancer Genome Atlas database. This study aimed to explore its roles and regulation mechanism in oral squamous cell carcinoma.

MATERIALS AND METHODS

We analyzed the expression of DLX6 and its association with overall survival in OSCC by real-time quantitative PCR. Besides, clone formation, proliferation, and apoptosis were detected after knocking down DLX6 and microarray analysis was performed to explore the possible regulatory mechanism.

RESULTS

DLX6 was overexpressed in oral cancer tissues and was associated with advance tumor stage and poor prognosis. In vitro studies have shown that DLX6 promotes proliferation and inhibits cell apoptosis in oral cancer cells. Microarray analysis along with Western blotting results indicated that DLX6 significantly associated with malignant tumors and may regulate OSCC cells proliferation through EGFR-CCND1 axis.

CONCLUSION

DLX6 promotes cell proliferation and suppresses cell apoptosis in oral cancer cells. EGFR-CCND1 pathway might be the potential mechanism participating in the regulating axis.

Secondary Palate Development in the Dog (Canis lupus familiaris)

OBJECTIVE

To investigate the gestational timing of morphologic events in normal canine secondary palate development as a baseline for studies in dog models of isolated cleft palate (CP).

METHODS

Beagle and beagle/cocker spaniel-hybrid fetal dogs were obtained by cesarean-section on various days of gestation, timed from the initial rise of serum progesterone concentration. Morphology of fetal heads was determined by examining serial coronal sections.

RESULTS

On gestational day 35 (d35), the palatal shelves pointed ventrally alongside the tongue. On d36, palatal shelves were elongated and elevated to a horizontal position above the tongue but were not touching. On d37, palatine shelves and vomer were touching, but the medial epithelial seam (MES) between the apposed shelves remained. Immunostaining with epithelial protein markers showed that the MES gradually dissolved and was replaced by mesenchyme during d37-d44, and palate fusion was complete by d44. Examination of remnant MES suggested that fusion of palatal shelves began in mid-palate and moved rostrally and caudally.

CONCLUSION

Palate development occurs in dogs in the steps described in humans and mice, but palate closure occurs at an intermediate time in gestation. These normative data will form the basis of future studies to determine pathophysiologic mechanisms in dog models of CP. Added clinical significance is the enhancement of dogs as a large animal model to test new approaches for palate repair, with the obvious advantage of achieving full maturity within 2 years rather than 2 decades.

Prenatal diagnosis of foetal hydrocephalus and suspected X-linked recessive inheritance of cleft lip in a Chihuahua

A 3.5-year-old, 2.9 kg, multiparous Chihuahua presented with abdominal distension; pregnancy was diagnosed. On Day 7 before parturition, prenatal sonograms showed anechoic bilateral dilated cerebral lateral ventricles, suggesting fluid-filled regions (ventriculomegaly) in one foetus. A Caesarean section was performed and the male newborn had an abnormally enlarged dome-shaped head and a cleft lip, and died 6 days after birth. According to the family pedigree, the X-linked recessive inheritance of an orofacial cleft from the unaffected mother was suggested. This report clearly demonstrates that canine foetal ventriculomegaly (hydrocephalus) can be diagnosed in utero. For dog breeds predisposed to congenital ventriculomegaly, early detection is important for the prediction of perinatal survival and adequate supportive care can be applied at delivery.

Incidence patterns of orofacial clefts in purebred dogs

Cleft lip (CL), cleft palate (CP) and cleft lip and palate (CLP) are the most common types of orofacial clefts in dogs. Orofacial clefts in dogs are clinically relevant because of the associated morbidity and high newborn mortality rate and are of interest as comparative models of disease. However, the incidence of CL, CP and CLP has not been investigated in purebred dogs, and the financial impact on breeders is unknown. The aims of this study were to document the incidence patterns of CL, CP and CLP in different breeds of dogs, determine whether defect phenotype is associated with skull type, genetic cluster and geographic location, and estimate the financial impact in breeding programs in the United States by means of an anonymous online survey. A total of 228 orofacial clefts were reported among 7,429 puppies whelped in the 12 preceding months. Breeds in the mastiff/terrier genetic cluster and brachycephalic breeds were predisposed to orofacial clefts. Certain breeds in the ancient genetic cluster were at increased odds of orofacial clefts. Male purebred dogs were at increased odds of CPs. Results confirm that brachycephalic breeds are overrepresented among cases of orofacial clefts. Furthermore, geographic region appeared to be a relevant risk factor and orofacial clefts represented a considerable financial loss to breeders. Improved understanding of the epidemiology of orofacial clefts (frequency, causes, predictors and risk factors) may help in identifying ways to minimize their occurrence. Information gained may potentially help veterinarians and researchers to diagnose, treat and prevent orofacial clefts.

Target Capture/Next-Generation Sequencing for Nonsyndromic Cleft Lip and Palate in the Japanese Population

OBJECTIVE

The pathogenesis of nonsyndromic cleft lip with or without cleft palate (NSCL ± P) and nonsyndromic cleft palate only (NSCP) may be associated with genetic factors. Although some predisposing genes/loci have been reported, their attributable risk is too small to be clinically meaningful. To clarify the genetic causes and mechanisms of NSCL±P or NSCP, we conducted mutation analysis of target genes using a next-generation sequencing (NGS) approach.

METHODS

The target genes, IRF6, WNT5A, WNT9B, TP63, MSX1, TFAP2A, PAX9, DLX3, DLX4, and MN1, were selected based on previous reports of potential associations with the development of NSCL±P or NSCP from genome-wide association studies and candidate gene analyses. Mutation analysis was conducted using NGS on 74 Japanese trios (patient and parents) and 18 Japanese patients only families.

RESULTS

We detected single-nucleotide variants (SNVs) for 7 genes: IRF6, DLX4, WNT5A, TFAP2A, WNT9B, TP63, and PAX9. The SNVs found on IRF6 and DLX4 were missense mutations, whereas those identified on WNT5A, TFAP2A, WNT9B, TP63, and PAX9 were rare variants in the noncoding region; no de novo mutation was identified in the trio samples. The amino acid change on DLX4 was detected within the highly conserved homeodomain and was predicted to have a deleterious impact on the protein function by in silico analysis.

CONCLUSIONS

The DLX4 missense mutation c.359C>T (Pro120Leu) was found in 1 Japanese patient with NSCL±P and was located in the homeodomain region. This mutation likely plays a role in the development of NSCL±P in the Japanese population.

Novel dental phenotype in non-syndromic Pierre Robin Sequence: A retrospective study

OBJECTIVE

The objective was to investigate dental phenotypes in individuals with non-syndromic Pierre Robin Sequence (ns-PRS) and compare the prevalence of these phenotypes with subjects with non-syndromic cleft palate (ns-CP) and a control group with subjects without any craniofacial anomalies.

METHODS

A total of 760 panoramic radiographs of 330 individuals (110 with ns-PRS; 110 with ns-CP and 110 without any malformations) were digitized and evaluated regarding the diagnosis of taurodontism, tooth agenesis, root dilaceration and tooth transposition. Chi-square test was applied to compare the occurrence of dental phenotypes between groups. A P value of less than 0.05 was considered statistically significant.

RESULTS

Total prevalence of dental phenotypes was 94.5% of ns-PRS; 54.5% of ns-CP and 59.1% of the control group subjects with a statistically significant difference for the ns-PRS when compared to the other two groups. Two dental phenotypes, taurodontism and dental agenesis were identified with statistically significant higher prevalences in subjects with ns-PRS when compared with the ns-CP group and the control group (p < 0.001). Taurodontism was the most prevalent dental phenotype, with 92.73% in the ns-PRS group, 40.91% for ns-CP and 44.55% in the control group. Tooth agenesis had a prevalence of 22.7% for ns-PRS, 4.5% for ns-CP and no case in the control group. For the prevalence of root dilaceration and tooth transposition, no statistically significant differences were observed between the three groups.

CONCLUSIONS

Due to the high frequency of taurodontism in individuals with ns-PRS, we suggested that this novel phenotype would be important in the phenotypic screening of ns-PRS and could be considered as a phenotype associated with ns-PRS.

Computed tomographic evaluation of cleft palate in one-day-old puppies

BACKGROUND

Cleft palate is a birth defect characterized by a lack of fusion between structures forming the palate. Causes include a multitude of factors, both genetic and environmental. Computed tomography (CT) is widely used to evaluate morphological features and diagnose head disorders in adult dogs. However, there is less data about its use in neonatal dogs. The purpose of this study was to perform CT evaluation of palatal defects in one-day-old puppies and to present a novel approach of 3D modeling in terms of cleft palate assessment.

RESULTS

Macroscopic and CT examinations were performed in 23 stillborn or euthanized purebred newborn puppies. On the basis of CT data, a 3D model was prepared and the cleft surface area was then calculated. A multi-stage approach, which utilised software such as 3D Slicer and Blender, was applied. Palatal defects were found in ten dogs, of which five had cleft palate, three had bilateral cleft lip and palate, one had a unilateral cleft lip and palate and one had a unilateral cleft lip. The surface area of the clefts ranged from 31 to 213 mm², which made up respectfully 11 to 63% of the total surface area of the palate. No abnormalities were found in thirteen dogs and they made up the control group.

CONCLUSIONS

Computed tomography and 3D modeling were very effective in evaluation of palatal disorders in newborn dogs. 3D models adapted to the natural curvature of the palate were created and more precise data was obtained. Morphological characteristics, CT findings and advanced image analysis of cleft palate in neonates obtained from these models increase the knowledge about this malformation in dogs.

A splice site variant in INPP5E causes diffuse cystic renal dysplasia and hepatic fibrosis in dogs

Ciliopathies presenting as inherited hepatorenal fibrocystic disorders are rare in humans and in dogs. We describe here a novel lethal ciliopathy in Norwich Terrier puppies that was diagnosed at necropsy and characterized as diffuse cystic renal disease and hepatic fibrosis. The histopathological findings were typical for cystic renal dysplasia in which the cysts were located in the straight portion of the proximal tubule, and thin descending and ascending limbs of Henle’s loop. The pedigree of the affected puppies was suggestive of an autosomal recessive inheritance and therefore, whole exome sequencing and homozygosity mapping were used for identification of the causative variant. The analyses revealed a case-specific homozygous splice donor site variant in a cilia related gene, INPP5E: c.1572+5G>A. Association of the variant with the defect was validated in a large cohort of Norwich Terriers with 3 cases and 480 controls, the carrier frequency being 6%. We observed that the identified variant introduces a novel splice site in INPP5E causing a frameshift and formation of a premature stop codon. In conclusion, our results suggest that the INPP5E: c.1572+5G>A variant is causal for the ciliopathy in Norwich Terriers. Therefore, genetic testing can be carried out in the future for the eradication of the disease from the breed.

Association Between DLX4 Polymorphisms and Nonsyndromic Orofacial Clefts in a Chinese Han Population

OBJECTIVE

Distal-less 4 ( DLX4) was recently identified as the causative gene for a syndromic form of cleft lip with or without cleft palate, and further biological analyses have established the importance of Dlx4 gene in craniofacial development, which suggested DLX4 as a promising candidate to further investigate any possible association between DLX4 polymorphisms and risk to nonsyndromic orofacial clefts (NSOFCs).

DESIGN

Single-nucleotide polymorphisms (SNPs) with minor allele frequency >5% in the Han Chinese population which locate in the 5' flanking region, 5'/3'-untranslated region, or coding region with nonsynonymous changes in DLX4 were selected. Four SNPs (rs58769681, rs1058562, rs1058564, and rs8066341) were thus included in the following genotyping using the TaqMan 5'-exonuclease allelic discrimination assay in a case-control cohort with 1522 individuals.

RESULTS

None of SNPs were associated with NSOFCat the allele and genotype levels in general and stratified single-marker analysis, including genotypic distributions under different modes of inheritance. In linkage disequilibrium (LD) analysis, we found strong LD ( r² > 0.8) between any 2 of the SNPs, respectively. Further haplotyping identified haplotypes C-C (formed by rs1058564 and rs1058562) and C-C-A (formed by rs1058564, rs1058562, and rs58769681) which reached the significance threshold ( P < .05); nevertheless, none of them survived the multiple comparison correction.

CONCLUSIONS

Our findings indicated the hypothesis that DLX4 variants contributing to NSOFC risk should be interpreted with caution. Further replications in diverse ethnic origins and larger cohorts are still warranted.

Breeding Soundness Examination of the Bitch

A breeding soundness examination is a vital part of any breeding program. These examinations are not performed as frequently in the bitch as they are in the male dog. They allow clinicians to identify any problems at an early stage in a bitch's breeding career and to screen for any genetic abnormalities. A thorough physical examination and accurate history guide the choice of which diagnostics tests are most useful. Ultrasound, culture, cytology, and biopsies (surgical and nonsurgical techniques) are discussed. Knowing which stage of the cycle to perform these diagnostics yields the most information and increases the chance of a successful outcome.

The ontogeny of Robin sequence

The triad of micrognathia, glossoptosis, and concomitant airway obstruction defined as "Robin sequence" (RS) is caused by oropharyngeal developmental events constrained by a reduced stomadeal space. This sequence of abnormal embryonic development also results in an anatomical configuration that might predispose the fetus to a cleft palate. RS is heterogeneous and many different etiologies have been described including syndromic, RS-plus, and isolated forms. For an optimal diagnosis, subsequent treatment and prognosis, a thorough understanding of the embryology and pathogenesis is necessary. This manuscript provides an update about our current understanding of the development of the mandible, tongue, and palate and possible mechanisms involved in the development of RS. Additionally, we provide the reader with an up-to-date summary of the different etiologies of this phenotype and link this to the embryologic, developmental, and genetic mechanisms.

Genetic analysis of optic nerve head coloboma in the Nova Scotia Duck Tolling Retriever identifies discordance with the NHEJ1 intronic deletion (collie eye anomaly mutation)

Collie eye anomaly (CEA) encompasses a spectrum of different ophthalmic phenotypes from clinically inconsequential choroidal hypoplasia to blindness from coloboma of the optic nerve head (ONH). A previous study found a 7.8-kb deletion in intron 4 of the NHEJ1 gene to be associated with CEA. A genetic test based on this association is recommended for many breeds, including the Nova Scotia Duck Tolling Retriever (NSDTR). Collection of ONH coloboma-affected NSDTR showed lack of concordance of the NHEJ1 intronic deletion with ONH coloboma. Using genomewide single nucleotide polymorphism (SNP) genotyping in 7 ONH coloboma-affected NSDTR cases and 47 unaffected NSDTR controls with no ophthalmic signs, one SNP, located on chromosome 7, demonstrated genomewide significance. However, high genomic inflation may have confounded the results. Therefore, the genomewide association study was repeated using EMMAX to control for population structure in the cohort of 7 cases and 47 controls. However, no regions of the genome were significantly associated with ONH coloboma. These results failed to document significant association with the CEA locus. Due to the complex genetic etiology of ONH coloboma, the NHEJ1 intronic deletion test results should be carefully considered when making breeding decisions. If the goal is to select for visually competent dogs, our data suggest that eye examinations of puppies would be more effective as a guide in selection of breeding pairs than relying solely on currently available genetic tests.

Digging for known genetic mutations underlying inherited bone and cartilage characteristics and disorders in the dog and cat

Gene mapping projects for many traits in both dogs and cats have yielded new knowledge. Both researchers and the public alike have been fascinated by the inheritance of breed characteristic phenotypes and sporadic disorders. It has been proposed that selective breeding practices have on occasion generated alterations in structure that might be harmful. In this review, simply inherited disorders and characteristics affecting bone and cartilage for which a putative mutation is known are collected. A better understanding of the known inherited basis of skeletal conditions and disorders will assist veterinarians to improve their diagnoses and increase their effectiveness on advising clients on the prevention, management, prognosis and possible treatment of the conditions.

Morphological evaluation of clefts of the lip, palate, or both in dogs

OBJECTIVE To systematically characterize the morphology of cleft lip, cleft palate, and cleft lip and palate in dogs. ANIMALS 32 client-owned dogs with clefts of the lip (n = 5), palate (23), or both (4) that had undergone a CT or cone-beam CT scan of the head prior to any surgical procedures involving the oral cavity or face. PROCEDURES Dog signalment and skull type were recorded. The anatomic form of each defect was characterized by use of a widely used human oral-cleft classification system on the basis of CT findings and clinical images. Other defect morphological features, including shape, relative size, facial symmetry, and vomer involvement, were also recorded. RESULTS 9 anatomic forms of cleft were identified. Two anatomic forms were identified in the 23 dogs with cleft palate, in which differences in defect shape and size as well as vomer abnormalities were also evident. Seven anatomic forms were observed in 9 dogs with cleft lip or cleft lip and palate, and most of these dogs had incisive bone abnormalities and facial asymmetry. CONCLUSIONS AND CLINICAL RELEVANCE The morphological features of congenitally acquired cleft lip, cleft palate, and cleft lip and palate were complex and varied among dogs. The features identified here may be useful for surgical planning, developing of clinical coding schemes, or informing genetic, embryological, or clinical research into birth defects in dogs and other species.

Zebrafish models of orofacial clefts

Zebrafish is a model organism that affords experimental advantages toward investigating the normal function of genes associated with congenital birth defects. Here we summarize zebrafish studies of genes implicated in orofacial cleft (OFC). The most common use of zebrafish in this context has been to explore the normal function an OFC-associated gene product in craniofacial morphogenesis by inhibiting expression of its zebrafish ortholog. The most frequently deployed method has been to inject embryos with antisense morpholino oligonucleotides targeting the desired transcript. However, improvements in targeted mutagenesis strategies have led to widespread adoption of CRISPR/Cas9 technology. A second application of zebrafish has been for functional assays of gene variants found in OFC patients; such in vivo assays are valuable because the success of in silico methods for testing allele severity has been mixed. Finally, zebrafish have been used to test the tissue specificity of enhancers that harbor single nucleotide polymorphisms associated with risk for OFC. We review examples of each of these approaches in the context of genes that are implicated in syndromic and non-syndromic OFC. Developmental Dynamics 246:897-914, 2017. © 2017 Wiley Periodicals, Inc.

A numerical classification system for cleft lip and palate in the dog

An easy-to-use classification that enables an accurate record of canine cleft lip and palate is fundamental for effective communication between professionals and researchers and optimal use of published information. Here we present how a classification system for human cleft lip and palate can be used to register spontaneous cases in dogs, highlighting its advantages. This system is based on four topographic areas with a numerical representation of the severity of the cleft in each area. The use of spontaneous cases has the advantage of providing clefts that are naturally similar to their human counterparts for surgical, genetic and genomic studies and, furthermore, will reduce the need for experimental models of this condition.

An intronic LINE-1 insertion in MERTK is strongly associated with retinopathy in Swedish Vallhund dogs

The domestic dog segregates a significant number of inherited progressive retinal diseases, several of which mirror human retinal diseases and which are collectively termed progressive retinal atrophy (PRA). In 2014, a novel form of PRA was reported in the Swedish Vallhund breed, and the disease was mapped to canine chromosome 17. The causal mutation was not identified, but expression analyses of the retinas of affected Vallhunds demonstrated a 6-fold increased expression of the MERTK gene compared to unaffected dogs. Using 24 retinopathy cases and 97 controls with no clinical signs of retinopathy, we replicated the chromosome 17 association in Swedish Vallhunds from the UK and aimed to elucidate the causal variant underlying this association using whole genome sequencing (WGS) of an affected dog. This revealed a 6-8 kb insertion in intron 1 of MERTK that was not present in WGS of 49 dogs of other breeds. Sequencing and BLASTN analysis of the inserted segment was consistent with the insertion comprising a full-length intact LINE-1 retroelement. Testing of the LINE-1 insertion for association with retinopathy in the UK set of 24 cases and 97 controls revealed a strong statistical association (P-value 6.0 x 10-11) that was subsequently replicated in the original Finnish study set (49 cases and 89 controls (P-value 4.3 x 10-19). In a pooled analysis of both studies (73 cases and 186 controls), the LINE-1 insertion was associated with a ~20-fold increased risk of retinopathy (odds ratio 23.41, 95% confidence intervals 10.99-49.86, P-value 1.3 x 10-27). Our study adds further support for regulatory disruption of MERTK in Swedish Vallhund retinopathy; however, further work is required to establish a functional overexpression model. Future work to characterise the mechanism by which this intronic mutation disrupts gene regulation will further improve the understanding of MERTK biology and its role in retinal function.

Congenital Malformations in River Buffalo (Bubalus bubalis)

Simple Summary

Congenital malformations (due to genetic causes) represent a hidden danger for animal production, above all when genetic selection is undertaken for production improvements. These malformations are responsible for economic losses either because they reduce the productivity of the farm, or because their spread in the population would decrease the total productivity of that species/breed. River buffalo is a species of increasing interest all over the world for its production abilities, as proved by the buffalo genome project and the genetic selection plans that are currently performed in different countries. The aim of this review is to provide a general view of different models of congenital malformations in buffalo and their world distribution. This would be useful either for those who performed buffalo genetic selection or for researchers in genetic diseases, which would be an advantage to their studies with respect to the knowledge of gene mutations and interactions in this species.

Abstract

The world buffalo population is about 168 million, and it is still growing, in India, China, Brazil, and Italy. In these countries, buffalo genetic breeding programs have been performed for many decades. The occurrence of congenital malformations has caused a slowing of the genetic progress and economic loss for the breeders, due to the death of animals, or damage to their reproductive ability or failing of milk production. Moreover, they cause animal welfare reduction because they can imply foetal dystocia and because the affected animals have a reduced fitness with little chances of survival. This review depicts, in the river buffalo (Bubalus bubalis) world population, the present status of the congenital malformations, due to genetic causes, to identify their frequency and distribution in order to develop genetic breeding plans able to improve the productive and reproductive performance, and avoid the spreading of detrimental gene variants. Congenital malformations most frequently reported in literature or signaled by breeders to the Department of Veterinary Medicine and Animal Production of the University Federico II (Naples, Italy) in river buffalo are: musculoskeletal defects (transverse hemimelia, arthrogryposis, umbilical hernia) and disorders of sexual development. In conclusion this review put in evidence that river buffalo have a great variety of malformations due to genetic causes, and TH and omphalocele are the most frequent and that several cases are still not reported, leading to an underestimation of the real weight of genetic diseases in this species.

A Novel Heterozygous Intragenic Sequence Variant in DLX6 Probably Underlies First Case of Autosomal Dominant Split-Hand/Foot Malformation Type 1

Split-hand and foot malformation (SHFM; MIM 183600) is a rare human genetic limb malformation. It is characterized by missing digital rays in the hands and feet. SHFMs vary in severity from mild abnormalities affecting a single limb to acute malformations involving all 4 limbs. It is inherited, as part of both a syndromic and nonsyndromic disorder, in an autosomal recessive, autosomal dominant, and X-linked patterns. So far, 9 loci of hand and foot malformation have been mapped on human chromosomes. The present study describes a family with 2 affected individuals segregating SHFM in an autosomal dominant fashion. Sanger sequencing of the genes involved in SHFM was performed to identify the disease-causing variant. Sequence analysis revealed the first heterozygous missense variant (c.632T>A, p.Val211Glu) in the distal-less homeobox 6 (DLX6) gene, located in chromosome 7q21, causing SHFM in the present family. This study supports the evidence of DLX6 as an SHFM-causing gene.

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.

Evaluation of the genetic basis of primary hypoadrenocorticism in Standard Poodles using SNP array genotyping and whole-genome sequencing

Primary hypoadrenocorticism, also known as Addison's disease, is an autoimmune disorder leading to the destruction of the adrenal cortex and subsequent loss of glucocorticoid and mineralocorticoid hormones. The disease is prevalent in Standard Poodles and is believed to be highly heritable in the breed. Using genotypes derived from the Illumina Canine HD SNP array, we performed a genome-wide association study of 133 carefully phenotyped Standard Poodles (61 affected, 72 unaffected) and found no markers significantly associated with the disease. We also sequenced the entire genomes of 20 Standard Poodles (13 affected, 7 unaffected) and analyzed the data to identify common variants (including SNPs, indels, structural variants, and copy number variants) across affected dogs and variants segregating within a single pedigree of highly affected dogs. We identified several candidate genes that may be fixed in both Standard Poodles and a small population of dogs of related breeds. Further studies are required to confirm these findings more broadly, as well as additional gene-mapping efforts aimed at fully understanding the genetic basis of what is likely a complex inherited disorder.

Whole-genome sequence, SNP chips and pedigree structure: building demographic profiles in domestic dog breeds to optimize genetic-trait mapping

In the decade following publication of the draft genome sequence of the domestic dog, extraordinary advances with application to several fields have been credited to the canine genetic system. Taking advantage of closed breeding populations and the subsequent selection for aesthetic and behavioral characteristics, researchers have leveraged the dog as an effective natural model for the study of complex traits, such as disease susceptibility, behavior and morphology, generating unique contributions to human health and biology. When designing genetic studies using purebred dogs, it is essential to consider the unique demography of each population, including estimation of effective population size and timing of population bottlenecks. The analytical design approach for genome-wide association studies (GWAS) and analysis of whole-genome sequence (WGS) experiments are inextricable from demographic data. We have performed a comprehensive study of genomic homozygosity, using high-depth WGS data for 90 individuals, and Illumina HD SNP data from 800 individuals representing 80 breeds. These data were coupled with extensive pedigree data analyses for 11 breeds that, together, allowed us to compute breed structure, demography, and molecular measures of genome diversity. Our comparative analyses characterize the extent, formation and implication of breed-specific diversity as it relates to population structure. These data demonstrate the relationship between breed-specific genome dynamics and population architecture, and provide important considerations influencing the technological and cohort design of association and other genomic studies.

Summary: Successful application of whole-genome sequencing and genome-wide association studies for identifying both loci and mutations in canines is influenced by breed structure and demography, motivating researchers to generate breed-specific strategies for canine genetic studies.

Dissection of the complex genetic basis of craniofacial anomalies using haploid genetics and interspecies hybrids in Nasonia wasps

The animal head is a complex structure where numerous sensory, structural and alimentary structures are concentrated and integrated, and its ontogeny requires precise and delicate interactions among genes, cells, and tissues. Thus, it is perhaps unsurprising that craniofacial abnormalities are among the most common birth defects in people, or that these defects have a complex genetic basis involving interactions among multiple loci. Developmental processes that depend on such epistatic interactions become exponentially more difficult to study in diploid organisms as the number of genes involved increases. Here, we present hybrid haploid males of the wasp species pair Nasonia vitripennis and Nasonia giraulti, which have distinct male head morphologies, as a genetic model of craniofacial development that possesses the genetic advantages of haploidy, along with many powerful genomic tools. Viable, fertile hybrids can be made between the species, and quantitative trail loci related to shape differences have been identified. In addition, a subset of hybrid males show head abnormalities, including clefting at the midline and asymmetries. Crucially, epistatic interactions among multiple loci underlie several developmental differences and defects observed in the F2 hybrid males. Furthermore, we demonstrate an introgression of a chromosomal region from N. giraulti into N. vitripennis that shows an abnormality in relative eye size, which maps to a region containing a major QTL for this trait. Therefore, the genetic sources of head morphology can, in principle, be identified by positional cloning. Thus, Nasonia is well positioned to be a uniquely powerful model invertebrate system with which to probe both development and complex genetics of craniofacial patterning and defects.

A multi-ethnic genome-wide association study identifies novel loci for non-syndromic cleft lip with or without cleft palate on 2p24.2, 17q23 and 19q13

Orofacial clefts (OFCs), which include non-syndromic cleft lip with or without cleft palate (CL/P), are among the most common birth defects in humans, affecting approximately 1 in 700 newborns. CL/P is phenotypically heterogeneous and has a complex etiology caused by genetic and environmental factors. Previous genome-wide association studies (GWASs) have identified at least 15 risk loci for CL/P. As these loci do not account for all of the genetic variance of CL/P, we hypothesized the existence of additional risk loci. We conducted a multiethnic GWAS in 6480 participants (823 unrelated cases, 1700 unrelated controls and 1319 case-parent trios) with European, Asian, African and Central and South American ancestry. Our GWAS revealed novel associations on 2p24 near FAM49A, a gene of unknown function (P = 4.22 × 10^-8), and 19q13 near RHPN2, a gene involved in organizing the actin cytoskeleton (P = 4.17 × 10^-8). Other regions reaching genome-wide significance were 1p36 (PAX7), 1p22 (ARHGAP29), 1q32 (IRF6), 8q24 and 17p13 (NTN1), all reported in previous GWASs. Stratification by ancestry group revealed a novel association with a region on 17q23 (P = 2.92 × 10^-8) among individuals with European ancestry. This region included several promising candidates including TANC2, an oncogene required for development, and DCAF7, a scaffolding protein required for craniofacial development. In the Central and South American ancestry group, significant associations with loci previously identified in Asian or European ancestry groups reflected their admixed ancestry. In summary, we have identified novel CL/P risk loci and suggest new genes involved in craniofacial development, confirming the highly heterogeneous etiology of OFCs.

The Influence of LINE-1 and SINE Retrotransposons on Mammalian Genomes

Transposable elements have had a profound impact on the structure and function of mammalian genomes. The retrotransposon Long INterspersed Element-1 (LINE-1 or L1), by virtue of its replicative mobilization mechanism, comprises ∼17% of the human genome. Although the vast majority of human LINE-1 sequences are inactive molecular fossils, an estimated 80-100 copies per individual retain the ability to mobilize by a process termed retrotransposition. Indeed, LINE-1 is the only active, autonomous retrotransposon in humans and its retrotransposition continues to generate both intra-individual and inter-individual genetic diversity. Here, we briefly review the types of transposable elements that reside in mammalian genomes. We will focus our discussion on LINE-1 retrotransposons and the non-autonomous Short INterspersed Elements (SINEs) that rely on the proteins encoded by LINE-1 for their mobilization. We review cases where LINE-1-mediated retrotransposition events have resulted in genetic disease and discuss how the characterization of these mutagenic insertions led to the identification of retrotransposition-competent LINE-1s in the human and mouse genomes. We then discuss how the integration of molecular genetic, biochemical, and modern genomic technologies have yielded insight into the mechanism of LINE-1 retrotransposition, the impact of LINE-1-mediated retrotransposition events on mammalian genomes, and the host cellular mechanisms that protect the genome from unabated LINE-1-mediated retrotransposition events. Throughout this review, we highlight unanswered questions in LINE-1 biology that provide exciting opportunities for future research. Clearly, much has been learned about LINE-1 and SINE biology since the publication of Mobile DNA II thirteen years ago. Future studies should continue to yield exciting discoveries about how these retrotransposons contribute to genetic diversity in mammalian genomes.

Reconstruction of Congenital Nose, Cleft Primary Palate, and Lip Disorders

Clefts of the primary palate in the dog are uncommon, and their repair can be challenging. The aims of this article are to provide information regarding pathogenesis and convey practical information for the repair of these defects.

New insights into craniofacial malformations

Development of the human skull and face is a highly orchestrated and complex three-dimensional morphogenetic process, involving hundreds of genes controlling the coordinated patterning, proliferation and differentiation of tissues having multiple embryological origins. Craniofacial malformations that occur because of abnormal development (including cleft lip and/or palate, craniosynostosis and facial dysostoses), comprise over one-third of all congenital birth defects. High-throughput sequencing has recently led to the identification of many new causative disease genes and functional studies have clarified their mechanisms of action. We present recent findings in craniofacial genetics and discuss how this information together with developmental studies in animal models is helping to increase understanding of normal craniofacial development.

DLX4 is associated with orofacial clefting and abnormal jaw development

Cleft lip and/or palate (CL/P) are common structural birth defects in humans. We used exome sequencing to study a patient with bilateral CL/P and identified a single nucleotide deletion in the patient and her similarly affected son—c.546_546delG, predicting p.Gln183Argfs*57 in the Distal-less 4 (DLX4) gene. The sequence variant was absent from databases, predicted to be deleterious and was verified by Sanger sequencing. In mammals, there are three Dlx homeobox clusters with closely located gene pairs (Dlx1/Dlx2, Dlx3/Dlx4, Dlx5/Dlx6). In situ hybridization showed that Dlx4 was expressed in the mesenchyme of the murine palatal shelves at E12.5, prior to palate closure. Wild-type human DLX4, but not mutant DLX4_c.546delG, could activate two murine Dlx conserved regulatory elements, implying that the mutation caused haploinsufficiency. We showed that reduced DLX4 expression after short interfering RNA treatment in a human cell line resulted in significant up-regulation of DLX3, DLX5 and DLX6, with reduced expression of DLX2 and significant up-regulation of BMP4, although the increased BMP4 expression was demonstrated only in HeLa cells. We used antisense morpholino oligonucleotides to target the orthologous Danio rerio gene, dlx4b, and found reduced cranial size and abnormal cartilaginous elements. We sequenced DLX4 in 155 patients with non-syndromic CL/P and CP, but observed no sequence variants. From the published literature, Dlx1/Dlx2 double homozygous null mice and Dlx5 homozygous null mice both have clefts of the secondary palate. This first finding of a DLX4 mutation in a family with CL/P establishes DLX4 as a potential cause of human clefts.

Role of region-distinctive expression of Rac1 in regulating fibronectin arrangement during palatal shelf elevation

Palatal shelf elevation is a crucial process in palate development, with the contribution of various factors. Disturbances in any factor during this process result in cleft palate. Prior to palatal shelf elevation starting from embryonic day 12.5, the Rac1 expression level in the bend region of the mid-palatal shelf progressively increases and the cell densities in the bend and groove regions gradually become higher than those in the middle region. The comparative decrease of cell density in the middle region is correlated with a gradual alteration of the arrangement of fibronectin (FN) fibers, whereas the bend and groove regions with higher cell densities maintain ring-like FN arrangements. Rac1 overexpression alters the fibrillar FN arrangement in the middle region to the ring-like arrangement by increasing cell density. This alteration is sufficient to induce the failure of palatal shelf elevation, ultimately leading to cleft palate. Furthermore, the inhibition of FN delays palatal shelf elevation. Thus, the spatiotemporal expression of Rac1 plays an impressive role in palatal shelf elevation by regulating FN arrangement within the palatal shelf.

Genome-wide association studies in dogs and humans identify ADAMTS20 as a risk variant for cleft lip and palate

Cleft lip with or without cleft palate (CL/P) is the most commonly occurring craniofacial birth defect. We provide insight into the genetic etiology of this birth defect by performing genome-wide association studies in two species: dogs and humans. In the dog, a genome-wide association study of 7 CL/P cases and 112 controls from the Nova Scotia Duck Tolling Retriever (NSDTR) breed identified a significantly associated region on canine chromosome 27 (unadjusted p=1.1 x 10^-13; adjusted p= 2.2 x 10^-3). Further analysis in NSDTR families and additional full sibling cases identified a 1.44 Mb homozygous haplotype (chromosome 27: 9.29 – 10.73 Mb) segregating with a more complex phenotype of cleft lip, cleft palate, and syndactyly (CLPS) in 13 cases. Whole-genome sequencing of 3 CLPS cases and 4 controls at 15X coverage led to the discovery of a frameshift mutation within ADAMTS20 (c.1360_1361delAA (p.Lys453Ilefs*3)), which segregated concordant with the phenotype. In a parallel study in humans, a family-based association analysis (DFAM) of 125 CL/P cases, 420 unaffected relatives, and 392 controls from a Guatemalan cohort, identified a suggestive association (rs10785430; p =2.67 x 10^-6) with the same gene, ADAMTS20. Sequencing of cases from the Guatemalan cohort was unable to identify a causative mutation within the coding region of ADAMTS20, but four coding variants were found in additional cases of CL/P. In summary, this study provides genetic evidence for a role of ADAMTS20 in CL/P development in dogs and as a candidate gene for CL/P development in humans.

Cleft lip with or without cleft palate (CL/P) is a commonly occurring birth defect that can lead to a lifetime of complications in affected children. To better understand the genetic cause of these disorders, we investigated CL/P in both dogs and humans. Genome-wide association studies in both species independently identify ADAMTS20 as a candidate gene for CL/P development. In dogs, a deletion within a functional domain of ADAMTS20 is responsible for CL/P in the Nova Scotia Duck Tolling Retriever dog breed. In humans, an associated region containing the same gene, ADAMTS20, was identified in a study population of native Guatemalans. Subsequent sequencing in humans was unable to identify a causative mutation within the coding region of ADAMTS20 in the Guatemalan cohort; however, sequencing of ADAMTS20 in additional cases with CL/P identified four novel coding variants. This work provides genetic evidence for a role for ADAMTS20 in CL/P development in both dogs and humans.

Analysis of the Relationship Between Micrognathia and Cleft Palate: A Systematic Review

Objective To gather data from relevant experimental and observational studies to determine the relationship between micrognathia and cleft palate. The goal is to raise awareness and motivate clinicians to consider the cause and effect relationship when confronted with patients with cleft palate, even if there is no clearly noticeable mandibular abnormality. Design Several electronic databases were systematically examined to find articles for this review, using search terms including "cleft palate," "micrognathia," "tongue," and "airway obstruction." PubMed was the source of all the articles chosen to be included. Exclusion criteria included case reports, articles focused on treatment options, and articles only tangentially related to cleft palate and/or micrognathia. Results A total of 930 articles were screened for relevance, and 82 articles were chosen for further analysis. Evidence gathered in this review includes a variety of etiological factors that are causative or associated with both micrognathia and cleft palate. Observational studies relating the two abnormalities are also included. Much of the included literature recognizes a cause-and-effect relationship between micrognathia and cleft palate. Conclusion On the basis of the published data, we suggest that micrognathia does induce cleft palate in humans and animals. With knowledge of this causative relationship, clinicians should consider the importance of gathering cephalometric data on the mandibles and tongues of patients presenting with isolated cleft palate to determine whether they have micrognathia as well. With more data, patterns may emerge that could give insight into the complex etiology of nonsyndromic cleft palate.

Loss-of-function mutation in the X-linked TBX22 promoter disrupts an ETS-1 binding site and leads to cleft palate

The cleft palate only (CPO) is a common congenital defect with complex etiology in humans. The molecular etiology of the CPO remains unknown. Here, we report a loss-of-function mutation in X-linked TBX22 gene (T-box 22) in a six-generation family of the CPO with obvious phenotypes of both cleft palate and hyper-nasal speech. We identify a functional -73G>A mutation in the promoter of TBX22, which is located at the core-binding site of transcription factor ETS-1 (v-ets avian erythroblastosis virus E26 oncogene homolog 1). Phylogenetic analysis showed that the sequence around the -73G>A mutation site is specific in primates. The mutation was detected in all five affected male members cosegregating with the affected phenotype and heterozygote occurred only in some unaffected females of the family, suggesting an X-linked transmission of the mutation in the family. The -73G>A variant is a novel single nucleotide mutation. Cell co-transfections indicated that ETS-1 could activate the TBX22 promoter. Moreover, EMSA and ChIP assays demonstrated that the allele A disrupts the binding site of ETS-1, thus markedly decreases the activity of the TBX22 promoter, which is likely to lead to the birth defect of the CPO without ankyloglossia. These results suggest that a loss-of-function mutation in the X-linked TBX22 promoter may cause the cleft palate through disruption of TBX22-ETS-1 pathway.