Gene-Gene Interaction Among WNT Genes for Oral Cleft in Trios

Applications and performance of artificial intelligence models in removable prosthodontics: A literature review

PURPOSE

In this narrative review, we present the current applications and performances of artificial intelligence (AI) models in different phases of the removable prosthodontic workflow and related research topics.

STUDY SELECTION

A literature search was conducted using PubMed, Scopus, Web of Science, and Google Scholar databases between January 2010 and January 2023. Search terms related to AI were combined with terms related to removable prosthodontics. Articles reporting the structure and performance of the developed AI model were selected for this literature review.

RESULTS

A total of 15 articles were relevant to the application of AI in removable prosthodontics, including maxillofacial prosthetics. These applications included the design of removable partial dentures, classification of partially edentulous arches, functional evaluation and outcome prediction in complete denture treatment, early prosthetic management of patients with cleft lip and palate, coloration of maxillofacial prostheses, and prediction of the material properties of denture teeth. Various AI models with reliable prediction accuracy have been developed using supervised learning.

CONCLUSIONS

The current applications of AI in removable prosthodontics exhibit significant potential for improving the prosthodontic workflow, with high accuracy levels reported in most of the reviewed studies. However, the focus has been predominantly on the diagnostic phase, with few studies addressing treatment planning and implementation. Because the number of AI-related studies in removable prosthodontics is limited, more models targeting different prosthodontic disciplines are required.

Harnessing the Power of Artificial Intelligence in Cleft Lip and Palate: An In-Depth Analysis from Diagnosis to Treatment, a Comprehensive Review

Cleft lip and palate (CLP) is the most common craniofacial malformation, with a range of physical, psychological, and aesthetic consequences. In this comprehensive review, our main objective is to thoroughly examine the relationship between CLP anomalies and the use of artificial intelligence (AI) in children. Additionally, we aim to explore how the integration of AI technology can bring about significant advancements in the fields of diagnosis, treatment methods, and predictive outcomes. By analyzing the existing evidence, we will highlight state-of-the-art algorithms and predictive AI models that play a crucial role in achieving precise diagnosis, susceptibility assessment, and treatment planning for children with CLP anomalies. Our focus will specifically be on the efficacy of alveolar bone graft and orthodontic interventions. The findings of this review showed that deep learning (DL) models revolutionize the diagnostic process, predict susceptibility to CLP, and enhance alveolar bone grafts and orthodontic treatment. DL models surpass human capabilities in terms of precision, and AI algorithms applied to large datasets can uncover the intricate genetic and environmental factors contributing to CLP. Additionally, Machine learning aids in preoperative planning for alveolar bone grafts and provides personalized treatment plans in orthodontic treatment. In conclusion, these advancements inspire optimism for a future where AI seamlessly integrates with CLP management, augmenting its analytical capabilities.

The presence and distribution of various genes in postnatal CLP-affected palatine tissue

BACKGROUND

Worldwide cleft lip with or without a cleft palate (CL/P) is the most common craniofacial birth defect. Apart from changes in facial appearance, additionally affected individuals often suffer from various associated comorbidities requiring complex multidisciplinary treatment with overall high expenses. Understanding the complete pathogenetic mechanisms of CL/P might aid in developing new preventative strategies and therapeutic approaches, help with genetic counselling, and improve quality of life. Many genes have been associated with the development of orofacial clefts; however, the majority require further research. Based on the role of PAX7, PAX9, SHH, SOX3, WNT3A, and WNT9B in orofacial development, the intention was to use chromogenic in situ hybridization to detect the six genes in postnatal CLP-affected palatine tissue and compare their distribution within the tissue samples.

RESULTS

Statistically significant differences in the distribution of PAX7, PAX9, WNT3A, and WNT9B were observed. In total, 19 pairs of moderate to very strong positive correlations were noted.

CONCLUSIONS

Changes in the cleft-affected palatine epithelium primarily seem to be associated with the PAX7 gene; however, PAX9, WNT3A, WNT9B, and SOX3 role seems to be more limited. Whilst connective tissue changes seem to depend on PAX7 only, SHH seems to participate individually and indistinctly. Numerous positive correlations reflect the complicating interactions of the pathways and their components in the orofacial cleft morphopathogenesis.

Identification of Novel Risk Variants of Non-Syndromic Cleft Palate by Targeted Gene Panel Sequencing

Non-syndromic cleft palate (ns-CP) has a genetically heterogeneous aetiology. Numerous studies have suggested a crucial role of rare coding variants in characterizing the unrevealed component of genetic variation in ns-CP called the "missing heritability". Therefore, this study aimed to detect low-frequency variants that are implicated in ns-CP aetiology in the Polish population. For this purpose, coding regions of 423 genes associated with orofacial cleft anomalies and/or involved with facial development were screened in 38 ns-CP patients using the next-generation sequencing technology. After multistage selection and prioritisation, eight novel and four known rare variants that may influence an individual's risk of ns-CP were identified. Among detected alternations, seven were located in novel candidate genes for ns-CP, including COL17A1 (c.2435-1G>A), DLG1 (c.1586G>C, p.Glu562Asp), NHS (c.568G>C, p.Val190Leu-de novo variant), NOTCH2 (c.1997A>G, p.Tyr666Cys), TBX18 (c.647A>T, p.His225Leu), VAX1 (c.400G>A, p.Ala134Thr) and WNT5B (c.716G>T, p.Arg239Leu). The remaining risk variants were identified within genes previously linked to ns-CP, confirming their contribution to this anomaly. This list included ARHGAP29 (c.1706G>A, p.Arg569Gln), FLNB (c.3605A>G, Tyr1202Cys), IRF6 (224A>G, p.Asp75Gly-de novo variant), LRP6 (c.481C>A, p.Pro161Thr) and TP63 (c.353A>T, p.Asn118Ile). In summary, this study provides further insights into the genetic components contributing to ns-CP aetiology and identifies novel susceptibility genes for this craniofacial anomaly.

GADGETS: a genetic algorithm for detecting epistasis using nuclear families

MOTIVATION

Epistasis may play an etiologic role in complex diseases, but research has been hindered because identification of interactions among sets of single nucleotide polymorphisms (SNPs) requires exploration of immense search spaces. Current approaches using nuclear families accommodate at most several hundred candidate SNPs.

RESULTS

GADGETS detects epistatic SNP-sets by applying a genetic algorithm to case-parent or case-sibling data. To allow for multiple epistatic sets, island subpopulations of SNP-sets evolve separately under selection for evident joint relevance to disease risk. The software evaluates the identified SNP-sets via permutation testing and provides graphical visualization. GADGETS correctly identified epistatic SNP-sets in realistically simulated case-parent triads with 10 000 candidate SNPs, far more SNPs than competitors can handle, and it outperformed competitors in simulations with many fewer SNPs. Applying GADGETS to family-based oral-clefting data from dbGaP identified SNP-sets with possible epistatic effects on risk.

AVAILABILITY AND IMPLEMENTATION

GADGETS is part of the epistasisGA package at https://github.com/mnodzenski/epistasisGA.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Current Applications of Artificial Intelligence in Cleft Care: A Scoping Review

Objective: This scoping review aims to identify the various areas and current status of the application of artificial intelligence (AI) for aiding individuals with cleft lip and/or palate.

Introduction: Cleft lip and/or palate contributes significantly toward the global burden on the healthcare system. Artificial intelligence is a technology that can help individuals with cleft lip and/or palate, especially those in areas with limited access to receive adequate care.

Inclusion Criteria: Studies that used artificial intelligence to aid the diagnosis, treatment, or its planning in individuals with cleft lip and/or palate were included.

Methodology: A search of the Pubmed, Embase, and IEEE Xplore databases was conducted using search terms artificial intelligence and cleft lip and/or palate. Gray literature was searched using Google Scholar. The study was conducted according to the PRISMA- ScR guidelines.

Results: The initial search identified 458 results, which were screened based on title and abstracts. After the screening, removal of duplicates, and a full-text reading of selected articles, 26 publications were included. They explored the use of AI in cleft lip and/or palate to aid in decisions regarding diagnosis, treatment, especially speech therapy, and prediction.

Conclusion: There is active interest and immense potential for the use of artificial intelligence in cleft lip and/or palate. Most studies currently focus on speech in cleft palate. Multi-center studies that include different populations, with collaboration amongst academicians and researchers, can further develop the technology.

Brief Survey on Machine Learning in Epistasis

In biology, the term "epistasis" indicates the effect of the interaction of a gene with another gene. A gene can interact with an independently sorted gene, located far away on the chromosome or on an entirely different chromosome, and this interaction can have a strong effect on the function of the two genes. These changes then can alter the consequences of the biological processes, influencing the organism's phenotype. Machine learning is an area of computer science that develops statistical methods able to recognize patterns from data. A typical machine learning algorithm consists of a training phase, where the model learns to recognize specific trends in the data, and a test phase, where the trained model applies its learned intelligence to recognize trends in external data. Scientists have applied machine learning to epistasis problems multiple times, especially to identify gene-gene interactions from genome-wide association study (GWAS) data. In this brief survey, we report and describe the main scientific articles published in data mining and epistasis. Our article confirms the effectiveness of machine learning in this genetics subfield.

[Evaluating the effect of WNT pathway genes considering interactions on the risk of non-syndromic oral clefts among Chinese populations]

OBJECTIVE

In this study, we used genome-wide association study (GWAS) data to explore whether WNT pathway genes were associated with non-syndromic oral clefts (NSOC) considering gene-gene interaction and gene-environment interaction.

METHODS

We conducted the analysis using 806 non-syndromic cleft lip with or without cleft palate (NSCL/P) case-parent trios and 202 non-syndromic cleft palate (NSCP) case-parent trios among Chinese populations selected from an international consortium established for a GWAS of non-syndromic oral clefts. Genotype data and maternal environmental exposures were collected through DNA samples and questionnaires. Conditional Logistic regression models were adopted to explore gene-gene interaction and gene-environment in teraction using trio package in R software. The threshold of significance level was set as 3.47×10^-4 using Bonferroni correction.

RESULTS

A total of 144 single nucleotide polymorphisms (SNPs) in seven genes passed the quality control process in NSCL/P trios and NSCP trios, respectively. Totally six pairs of SNPs interactions showed statistically significant SNP-SNP interaction (P < 3.47×10^-4) after Bonferroni correction, which were rs7618735 (WNT5A) and rs10848543 (WNT5B), rs631948 (WNT11) and rs556874 (WNT5A), and rs631948 (WNT11) and rs472631 (WNT5A) among NSCL/P trios; rs589149 (WNT11) and rs4765834 (WNT5B), rs1402704 (WNT11) and rs358792 (WNT5A), and rs1402704 (WNT11) and rs358793 (WNT5A) among NSCP trios, respectively. In addition, no significant result was found for gene-environment interaction analysis in both of the NSCL/P trios and NSCP trios.

CONCLUSION

Though this study failed to detect significant association based on gene-environment interactions of seven WNT pathway genes and the risk of NSOC, WNT pathway genes may influence the risk of NSOC through potential gene-gene interaction.

Gene-gene interactions between BMP4 and ARHGAP29 among non-syndromic cleft lip only (NSCLO) trios from western Han Chinese population

BACKGROUND

Genome-wide association studies (GWAS) have found more than 20 genes associated with a risk of non-syndromic cleft lip with or without cleft palate (NSCL/P). However, the interactions between these risk genes have been rarely reported.

METHODS

Here we selected 47 Single Nucleotide Polymorphisms (SNP) from previous GWASs and tested for possible interactions among 302 NSCL/P case-parent trios from a western Han Chinese population to further explore the genetic etiology of NSCL/P. Conditional logistic regression models were performed including gene-gene (G×G) interaction.

RESULTS

Twenty pairwise interactions yielded significant p-values. Most of the signals of interaction between the SNPs were detected at the same gene including v-maf musculoaponeurotic fibrosarcoma oncogene family, protein B (MAFB), netrin 1 (NTN1), and single nucleotide polymorphic marker within interferon regulatory factor 6 (IRF6). We found evidence of the interaction between rs17563 (bone morphogenetic protein 4, BMP4) and rs560426 (subfamily A member 4/Rho GTPase activating protein 29, ARHGAP29) (P=0.00093) in NSCLO trios.

CONCLUSIONS

Gene-gene interaction between markers in BMP4 and ARHGAP29 may influence the risk of NSCLO in western Han Chinese population, which might explain the missing heritability for NSCL/P.

PBX-WNT-P63-IRF6 pathway in nonsyndromic cleft lip and palate

Nonsyndromic cleft lip and palate (NSCLP) is one of the most common craniofacial anomalies in humans, affecting more than 135,000 newborns worldwide. NSCLP has a multifactorial etiology with more than 50 genes postulated to play an etiologic role. The genetic pathway comprised of Pbx-Wnt-p63-Irf6 genes was shown to control facial morphogenesis in mice and proposed as a regulatory pathway for NSCLP. Based on these findings, we investigated whether variation in PBX1, PBX2, and TP63, and their proposed interactions were associated with NSCLP. Fourteen single nucleotide variants (SNVs) in/nearby PBX1, PBX2, and TP63 were genotyped in 780 NSCLP families of nonHispanic white (NHW) and Hispanic ethnicities. Family-based association tests were performed for individual SNVs stratified by ethnicity and family history of NSCLP. Gene-gene interactions were also tested. A significant association was found for PBX2 rs3131300 and NSCLP in combined Hispanic families (p = .003) while nominal association was found for TP63 rs9332461 in multiplex Hispanic families (p = .005). Significant haplotype associations were observed for PBX2 in NHW (p = .0002) and Hispanic families (p = .003), and for TP63 in multiplex Hispanic families (.003). An independent case-control group was used to validate findings, and significant associations were found with PBX1 rs6426870 (p = .007) and TP63 rs9332461 (p = .03). Gene-gene interactions were detected between PBX1/PBX2/TP63 with IRF6 in NHW families, and between PBX1 with WNT9B in both NHW and Hispanic families (p < .0018). This study provides the first evidence for a role of PBX1 and PBX2, additional evidence for the role of TP63, and support for the proposed PBX-WNT-TP63-IRF6 regulatory pathway in the etiology of NSCLP.

Gene-gene interaction among cell adhesion genes and risk of nonsyndromic cleft lip with or without cleft palate in Chinese case-parent trios

Background

Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is a common birth defect with complex etiology. One strategy for studying the genetic risk factors of NSCL/P is to consider gene–gene interaction (G × G) among gene pathways having a role in craniofacial development. The present study aimed to investigate the G × G among cell adhesion gene pathway.

Methods

We carried out an interaction analysis of eight genes involved in cell adherens junctions among 806 NSCL/P Chinese case‐parent trios originally recruited for a genome‐wide association study (GWAS). Regression‐based approach was used to test for two‐way G × G interaction, while machine learning algorithm was run for exploring both two‐way and multi‐way interaction that may affect the risk of NSCL/P.

Results

A two‐way ACTN1 × CTNNB1 interaction reached the adjusted significance level. The single nucleotide polymorphisms pair composed of rs17252114 (CTNNB1) and rs1274944 (ACTN1) yielded a p value of .0002, and this interaction was also supported by the logic regression algorithm. Higher order interactions involving ACTN1, CTNNB1, and CDH1 were picked out by logic regression, suggesting a potential role in NSCL/P risk.

Conclusion

This study suggests for the first time evidence of both two‐way and multi‐way G × G interactions among cell adhesion genes contributing to the NSCL/P risk.

Polymorphic Variants of V-Maf Musculoaponeurotic Fibrosarcoma Oncogene Homolog B (rs13041247 and rs11696257) and Risk of Non-Syndromic Cleft Lip/Palate: Systematic Review and Meta-Analysis

Background: Non-syndromic cleft lip/palate (NSCL/P) has an etiology, including both genetic and environmental factors. Herein, we evaluated the association of rs13041247 and rs11696257 v-maf musculoaponeurotic fibrosarcoma oncogene homolog B (MAFB) polymorphisms with the risk of NSCL/P in a meta-analysis. Methods: The PubMed/Medline, Scopus, Cochrane Library, Web of Science, and HuGE Navigator databases were systematically searched to retrieve relevant articles published up to January 2019. The Newcastle–Ottawa scale was applied for quality evaluation of retrieved articles. The 95% confidence interval (CI) and crude odds ratio (OR) were calculated for each study using the Review Manager 5.3 software to show the association between MAFB polymorphisms and risk of NSCL/P. The comprehensive meta-analysis 2.0 software was used to calculate the publication bias. In addition, sensitivity analysis was carried out to show the stability of results. Results: Of 102 articles retrieved from the databases, 10 articles were analyzed in this meta-analysis. Ten articles, including eleven studies reporting rs13041247 MAFB polymorphism, included 3082 NSCL/P patients and 4104 controls. Three studies that reported rs11696257 MAFB polymorphism involved 845 NSCL/P patients and 927 controls. The rs11696257 MAFB polymorphism was not associated with the risk of NSCL/P, but the CC and TC genotypes of rs13041247 polymorphism were associated with the risk of NSCL/P. Nevertheless, the C allele and CC and TC genotypes were associated with a significant decline in the risk of NSCL/P in population-based studies. Conclusions: The results of this meta-analysis demonstrated that the risk of NSCL/P was related to rs13041247 polymorphism, not rs11696257 MAFB polymorphism. Well-designed studies are required to assess the interaction of MAFB and other genes with environmental factors in different ethnic groups.

Exploring the interaction between FGF Genes and T-box genes among chinese nonsyndromic cleft lip with or without cleft palate case-parent trios

Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is a common birth defect. Genetic variants causing syndromic orofacial clefts can also contribute to the etiology of NSCL/P. The purpose of the present study was to explore gene-gene (G × G) interaction using common single nucleotide polymorphic (SNP) markers in fibroblast growth factor (FGF) family and its receptors and T-box genes, which were associated with syndromic orofacial clefts. Our study was conducted in 806 Chinese NSCL/P case-parent trios drawn from an international consortium. A total of 252 SNPs in FGF8, FGF10, FGFR1, FGFR2, and TBX5 passed the quality control criteria and were included in the analysis. The interactions between SNPs in different genes were assessed using Cordell's method, which fitted a conditional logistic regression model. The analysis was performed using the R-package trio (Version 3.8.0). Bonferroni correction was used to adjust for multiple comparisons, and the overall significance threshold was set as P = 1.98 × 10^-4 (0.05/252). Conditional logistic regression revealed the most significant interaction between rs2330542 in FGF10 and rs1946295 in TBX5, which remained significant (P = 9.63 × 10^-6 ) after Bonferroni correction. The relative risk of allele C in rs2330542 (FGF10) was 1.02 (95%CI 0.81-1.28), while the relative risk was 1.42 (95%CI 1.03-1.97) when the exposure was a combination of allele C in rs2330542 and allele A in rs1946295 (TBX5). Our findings confirmed the importance of considering G × G interaction when exploring the genetic risk factors of NSCL/P. Further investigations are warranted to validate the potential interaction and reveal the biological function of FGF10/FGFR2/TBX5. Environ. Mol. Mutagen. 2019. © 2019 Wiley Periodicals, Inc.

Exon sequencing reveals that missense mutation of PBX1 gene may increase the risk of non-syndromic cleft lip/palate

OBJECTIVE

Non-syndromic oral cleft (NSOC) is one of the most common multifactorial birth defects. A previous animal study showed PBX1 gene knockout mice consequently exhibited complete cleft lip/palate (CL/P). However, little is known about the association between PBX1 and NSOC in humans. This study investigated the role of the PBX1 gene in NSOC in the Han Chinese population.

METHODS

In all, 287 NSOCs were recruited for this study. First, exons in the PBX1 gene were sequenced among 50 non-syndromic cleft lip and palate cases to screen for variations by the Sanger sequencing method. Then, we selected four SNPs to replicate among 237 NSOC trios and analyzed the data by using TDT and parent of origin effect methods.

RESULTS

Exon sequencing identified six variants of the PBX1 gene. Among them, four variants were common variants. TDT analysis revealed allele G at rs2275558 and allele T at rs3835581 were over-transmitted in NSCL/P (P=0.039 and 0.038, respectively), which could increase the risk for NSCL/P. Parent of origin effect analysis indicated that allele G at rs2275558 was paternally over-transmitted for NSCL/P (P=0.0091).

CONCLUSION

This is the first report that the PBX1 gene is associated with NSCL/P, which indicates that it is a promising candidate gene for NSCL/P.

Genetic interactions between Ror2 and Wnt9a, Ror1 and Wnt9a and Ror2 and Ror1: Phenotypic analysis of the limb skeleton and palate in compound mutants

Mutations in the human receptor tyrosine kinase ROR2 are associated with Robinow syndrome (RRS) and brachydactyly type B1. Amongst others, the shortened limb phenotype associated with RRS is recapitulated in Ror2^-/- mutant mice. In contrast, Ror1^-/- mutant mice are viable and show no limb phenotype. Ror1^-/- ;Ror2^-/- double mutants are embryonic lethal, whereas double mutants containing a hypomorphic Ror1 allele (Ror1^hyp ) survive up to birth and display a more severe shortened limb phenotype. Both orphan receptors have been shown to act as possible Wnt coreceptors and to mediate the Wnt5a signal. Here, we analyzed genetic interactions between the Wnt ligand, Wnt9a, and Ror2 or Ror1, as Wnt9a has also been implicated in skeletal development. Wnt9a^-/- single mutants display a mild shortening of the long bones, whereas these are severely shortened in Ror2^-/- mutants. Ror2^-/- ;Wnt9a^-/- double mutants displayed even more severely shortened long bones, and intermediate phenotypes were observed in compound Ror2;Wnt9a mutants. Long bones were also shorter in Ror1^hyp/hyp ;Wnt9a^-/- double mutants. In addition, Ror1^hyp/hyp ;Wnt9a^-/- double mutants displayed a secondary palate cleft phenotype, which was not present in the respective single mutants. Interestingly, 50% of compound mutant pups heterozygous for Ror2 and homozygous mutant for Ror1 also developed a secondary palate cleft phenotype.

Wnt signaling in orofacial clefts: crosstalk, pathogenesis and models

Diverse signaling cues and attendant proteins work together during organogenesis, including craniofacial development. Lip and palate formation starts as early as the fourth week of gestation in humans or embryonic day 9.5 in mice. Disruptions in these early events may cause serious consequences, such as orofacial clefts, mainly cleft lip and/or cleft palate. Morphogenetic Wnt signaling, along with other signaling pathways and transcription regulation mechanisms, plays crucial roles during embryonic development, yet the signaling mechanisms and interactions in lip and palate formation and fusion remain poorly understood. Various Wnt signaling and related genes have been associated with orofacial clefts. This Review discusses the role of Wnt signaling and its crosstalk with cell adhesion molecules, transcription factors, epigenetic regulators and other morphogenetic signaling pathways, including the Bmp, Fgf, Tgfβ, Shh and retinoic acid pathways, in orofacial clefts in humans and animal models, which may provide a better understanding of these disorders and could be applied towards prevention and treatments.

Gene-Gene Interactions among SPRYs for Nonsyndromic Cleft Lip/Palate

Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is a common birth defect with a complex genetic architecture. Gene-gene interactions have been increasingly regarded as contributing to the etiology of NSCL/P. A recent genome-wide association study revealed that a novel single-nucleotide polymorphism at SPRY1 in 4q28.1 showed a significant association with NSCL/P. In the current study, we explored the role of 3 SPRY genes in the etiology of NSCL/P by detecting gene-gene interactions: SPRY1, SPRY2, and SPRY4-with SPRY3 excluded due to its special location on the X chromosome. We selected markers in 3 SPRY genes to test for gene-gene interactions using 1,908 case-parent trios recruited from an international consortium established for a genome-wide association study of nonsyndromic oral clefts. As the trios came from populations with different ancestries, subgroup analyses were conducted among Europeans and Asians. Cordell's method based on conditional logistic regression models was applied to test for potential gene-gene interactions via the statistical package TRIO in R software. Gene-gene interaction analyses yielded 10 pairs of SNPs in Europeans and 6 pairs in Asians that achieved significance after Bonferroni correction. The significant interactions were confirmed in the 10,000-permutation tests (empirical P = 0.003 for the most significant interaction). The study identified gene-gene interactions among SPRY genes among 1,908 NSCL/P trios, which revealed the importance of potential gene-gene interactions for understanding the genetic architecture of NSCL/P. The evidence of gene-gene interactions in this study also provided clues for future biological studies to further investigate the mechanism of how SPRY genes participate in the development of NSCL/P.

Gene-gene interaction for nonsyndromic cleft lip with or without cleft palate in Chilean case-parent trios

OBJECTIVE

Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is a birth defect for which several genes susceptibility genes been proposed. Consequently, it has been suggested that many of these genes belong to common inter-related pathways during craniofacial development gene-gene interaction. We evaluated the presence of gene-gene interaction for single nucleotide polymorphisms within interferon regulatory factor 6 (IRF6), muscle segment homeobox 1 (MSX1), bone morphogenetic protein 4 (BMP4) and transforming growth factor 3 (TGFB3) genes in NSCL/P risk in Chilean case-parent trios.

DESIGN

From previous studies, we retrieved genotypes for 13 polymorphic variants within these four genes in 152 case-parent trios. Using the trio package (R) we evaluate the gene-gen interaction in genetic markers pairs applying a 1°-of-freedom test (1df) and a confirmatory 4°-of-freedom (4df) test for epistasis followed by both a permutation test and a Benjamini-Hochberg test for multiple comparisons adjustment.

RESULTS

We found evidence of gene-gene interaction for rs6446693 (MSX1) and rs2268625 (TGFB3) (4df p = 0.024; permutation p = 0.015, Benjamini-Hochberg p = 0.001).

CONCLUSIONS

A significant gene-gene interaction was detected for rs6446693 (MSX1) and rs2268625 (TGFB3). This finding is concordant with research in animal models showing that MSX1 and TGFB3 are expressed in common molecular pathways acting in an epistatic manner during maxillofacial development.

Evaluating the effect of nicotinic cholinergic receptor genes on the risk of nonsyndromic cleft lip with or without cleft palate

OBJECTIVE

Multiple studies have suggested nonsyndromic cleft lip with or without cleft palate (NSCL/P), and lung cancer may have common genetic etiology. Previous studies have showed genetic variants in nicotinic cholinergic receptor genes (CHRNs) may influence risk of lung cancer. We aimed to explore the effect of CHRNs on risk of NSCL/P considering gene-gene (GxG) interaction for these genes.

SUBJECTS AND METHODS

We selected 120 markers in 14 CHRNs to test for GxG interaction using 806 Chinese case-parent trios recruited from an international consortium established for a GWAS of oral clefts.

RESULTS

Totally, two pairs of SNPs yielded significant GxG interactions after Bonferroni correction (rs935865 and rs2337980 with p = 4.04 × 10^-5 , rs2741335 and rs3743077 with p = 4.80 × 10^-4 ), and these pairwise interactions were confirmed in permutation tests. In addition, the relative risk (RR) of the putative interaction between rs935865 and rs2337980 was 1.10 (95% CI: 0.92~1.31).

CONCLUSIONS

While the single SNP association and the gene-environment interaction analysis of 14 CHRN genes yielded no signal, this study did demonstrate the importance of considering potential GxG interaction for exploring etiology of NSCL/P. This study suggests an important role for particular combinations of SNPs in CHRN genes in influencing risk to NSCL/P, which needs further study.

Evidence of interaction between genes in the folate/homocysteine metabolic pathway in controlling risk of non-syndromic oral cleft

OBJECTIVE

Little consistent evidence is available for the association between the risk of non-syndromic cleft lip with or without cleft palate (NSCL/P) and any of the individual genes in the folate/homocysteine metabolic pathway. We investigated the genes in the folate pathway to further clarify its potential influence on the risk of NSCL/P considering gene-gene (G×G) interaction.

SUBJECTS AND METHODS

We selected markers in 18 genes from the pathway and applied Cordell's method to test for G×G interaction using 1,908 NSCL/P case-parent trios ascertained in an international consortium where a genomewide association study (GWAS) of oral clefts was conducted.

RESULTS

We found intriguing signals among Asian and European ancestry groups for G×G interaction between markers in betaine-homocysteine methyltransferase gene (BHMT/BHMT2) and dimethylglycine dehydrogenase gene (DMGDH) attaining genomewide significance. In the pooled data, the top significant interaction was found between rs13158309 (BHMT) and rs10514154 (DMGDH, p = 1.45 × 10^-12 ).

CONCLUSIONS

Our study illustrated the importance of taking into account potential G×G interaction for genetic association analysis in NSCL/P, and this study suggested both BHMT/BHMT2 and DMGDH should be considered as candidate genes for NSCL/P in future studies.

Gene-gene interaction between MSX1 and TP63 in Asian case-parent trios with nonsyndromic cleft lip with or without cleft palate

BACKGROUND

Small ubiquitin-like modification, also known as sumoylation, is a crucial post-translational regulatory mechanisms involved in development of the lip and palate. Recent studies reported two sumoylation target genes, MSX1 and TP63, to have achieved genome-wide level significance in tests of association with nonsyndromic clefts. Here, we performed a candidate gene analysis considering gene-gene and gene-environment interaction for SUMO1, MSX1, and TP63 to further explore the etiology of nonsyndromic cleft lip with or without cleft palate (NSCL/P).

METHODS

A total of 130 single-nucleotide polymorphisms (SNPs) in or near SUMO1, MSX1, and TP63 was analyzed among 1,038 Asian NSCL/P trios ascertained through an international consortium. Conditional logistic regression models were used to explore gene-gene (G × G) and gene-environment (G × E) interaction involving maternal environmental tobacco smoke and multivitamin supplementation. Bonferroni correction was used for G × E analysis and permutation tests were used for G × G analysis.

RESULTS

While transmission disequilibrium tests and gene-environment interaction analysis showed no significant results, we did find signals of gene-gene interaction between SNPs near MSX1 and TP63. Three pairwise interactions yielded significant p values in permutation tests (rs884690 and rs9290890 with p = 9.34 × 10^-5 and empirical p = 1.00 × 10^-4 , rs1022136 and rs4687098 with p = 2.41 × 10^-4 and empirical p = 2.95 × 10^-4 , rs6819546 and rs9681004 with p = 5.15 × 10^-4 and empirical p = 3.02 × 10^-4 ).

CONCLUSION

Gene-gene interaction between MSX1 and TP63 may influence the risk of NSCL/P in Asian populations. Our study provided additional understanding of the genetic etiology of NSCL/P and underlined the importance of considering gene-gene interaction in the etiology of this common craniofacial malformation.

Genotype-driven identification of a molecular network predictive of advanced coronary calcium in ClinSeq® and Framingham Heart Study cohorts

BACKGROUND

One goal of personalized medicine is leveraging the emerging tools of data science to guide medical decision-making. Achieving this using disparate data sources is most daunting for polygenic traits. To this end, we employed random forests (RFs) and neural networks (NNs) for predictive modeling of coronary artery calcium (CAC), which is an intermediate endo-phenotype of coronary artery disease (CAD).

METHODS

Model inputs were derived from advanced cases in the ClinSeq®; discovery cohort (n=16) and the FHS replication cohort (n=36) from 89 th -99 th CAC score percentile range, and age-matched controls (ClinSeq®; n=16, FHS n=36) with no detectable CAC (all subjects were Caucasian males). These inputs included clinical variables and genotypes of 56 single nucleotide polymorphisms (SNPs) ranked highest in terms of their nominal correlation with the advanced CAC state in the discovery cohort. Predictive performance was assessed by computing the areas under receiver operating characteristic curves (ROC-AUC).

RESULTS

RF models trained and tested with clinical variables generated ROC-AUC values of 0.69 and 0.61 in the discovery and replication cohorts, respectively. In contrast, in both cohorts, the set of SNPs derived from the discovery cohort were highly predictive (ROC-AUC ≥0.85) with no significant change in predictive performance upon integration of clinical and genotype variables. Using the 21 SNPs that produced optimal predictive performance in both cohorts, we developed NN models trained with ClinSeq®; data and tested with FHS data and obtained high predictive accuracy (ROC-AUC=0.80-0.85) with several topologies. Several CAD and "vascular aging" related biological processes were enriched in the network of genes constructed from the predictive SNPs.

CONCLUSIONS

We identified a molecular network predictive of advanced coronary calcium using genotype data from ClinSeq®; and FHS cohorts. Our results illustrate that machine learning tools, which utilize complex interactions between disease predictors intrinsic to the pathogenesis of polygenic disorders, hold promise for deriving predictive disease models and networks.

Gene-gene interaction of single nucleotide polymorphisms in 16p13.3 may contribute to the risk of non-syndromic cleft lip with or without cleft palate in Chinese case-parent trios

Non-syndromic cleft lip with or without cleft palate (NSCL/P) is a common birth defect with a complex and heterogeneous etiology. A recent genome-wide association study (GWAS) among Chinese populations has identified a new region at 16p13.3 as being associated with NSCL/P, which requires further replication. Here, we attempted to replicate and further clarify the genetic association between this region and NSCL/P, as well as testing for potential gene-gene (G × G) and gene-environment (G × E) interactions. We conducted transmission disequilibrium tests on 69 single nucleotide polymorphisms (SNPs) mapping to 16p13.3 among 806 Chinese case-parent trios ascertained through an international consortium where a GWAS of oral clefts was conducted. G × G, as well as G × E interactions involving maternal environmental tobacco smoke (ETS) and multivitamin supplementation, were explored using conditional logistic regression model. We applied Cordell's method as implemented in the R package TRIO to test for possible interactions. While no SNPs showed evidence of linkage and association with NSCL/P after Bonferroni correction, we found signals of G × G interactions between SNPs in 16p13.3. Nine pairs of SNP-SNP interactions attained significance after Bonferroni correction, among which the most significant interaction was found between rs2072346 (ADCY9) and rs11646137 (intergenic region, P = 7.2 × 10^-5 ). Linkage disequilibrium (LD) analysis revealed only low level of LD between these SNPs. This study failed to confirm the significant association between SNPs within 16p13.3 and the risk of NSCL/P, but underlined the importance of taking into account potential G × G interactions for the genetic association analysis of NSCL/P.

Evidence for SNP-SNP interaction identified through targeted sequencing of cleft case-parent trios

Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is the most common craniofacial birth defect in humans, affecting 1 in 700 live births. This malformation has a complex etiology where multiple genes and several environmental factors influence risk. At least a dozen different genes have been confirmed to be associated with risk of NSCL/P in previous studies. However, all the known genetic risk factors cannot fully explain the observed heritability of NSCL/P, and several authors have suggested gene-gene (G × G) interaction may be important in the etiology of this complex and heterogeneous malformation. We tested for G × G interactions using common single nucleotide polymorphic (SNP) markers from targeted sequencing in 13 regions identified by previous studies spanning 6.3 Mb of the genome in a study of 1,498 NSCL/P case-parent trios. We used the R-package trio to assess interactions between polymorphic markers in different genes, using a 1 degree of freedom (1df) test for screening, and a 4 degree of freedom (4df) test to assess statistical significance of epistatic interactions. To adjust for multiple comparisons, we performed permutation tests. The most significant interaction was observed between rs6029315 in MAFB and rs6681355 in IRF6 (4df P = 3.8 × 10^-8 ) in case-parent trios of European ancestry, which remained significant after correcting for multiple comparisons. However, no significant interaction was detected in trios of Asian ancestry.

Genetic variants of 20q12 contributed to non-syndromic orofacial clefts susceptibility

OBJECTIVE

Previous genomewide association studies (GWAS) identified a region near MAFB at chr20q12 associated with non-syndromic orofacial clefts (NSOC) susceptibility. However, whether other SNPs in this area could independently contribute to non-syndromic orofacial clefts in Chinese populations remained obscure.

MATERIALS AND METHODS

We selected 24 SNPs based on a haplotype-tagging SNP strategy and evaluated their associations with risk of non-syndromic orofacial clefts in a large-scale two-stage case-control study with 1278 cases and 1295 controls. Genotyping was performed with Sequenom and TaqMan assay. Associations between the SNPs and risk of non-syndromic orofacial clefts were estimated from unconditional logistic regression analyses.

RESULTS

Overall, six SNPs were found to be the susceptible factors of non-syndromic orofacial clefts. The most significant and independent SNP was rs6129653 (additive model of P value = 1.4E-06). In subgroup analysis, its significant associations with cleft lip only (CLO) and cleft lip and palate (CLP) were observed. Furthermore, in silico bioinformatics analysis indicated that rs6129653 was located in the transcriptionally active region and associated with MAFB expression in human brain tissues.

CONCLUSIONS

Rs6129653 was an independent locus of non-syndromic orofacial clefts among Chinese populations possibly due to its potential of distal transcriptional regulation of MAFB expression.

Gene Interactions Provide Evidence for Signaling Pathways Involved in Cleft Lip/Palate in Humans

Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is a common craniofacial birth defect that has a complex etiology. Genome-wide association studies have recently identified new loci associated with NSCL/P, but these loci have not been analyzed in a Mexican Mestizo population. A complex etiology implies the presence of genetic interactions, but there is little available information regarding this in NSCL/P, and no signaling pathway has been clearly implicated in humans. Here, we analyzed the associations of 24 single nucleotide polymorphisms (SNPs) with NSCL/P in a Mexican Mestizo population (133 cases, 263 controls). The multifactorial dimensionality reduction method was used to examine gene-gene and gene-folic acid consumption interactions for the 24 SNPs analyzed in this study and for 2 additional SNPs that had previously been genotyped in the same study population. Six SNPs located in paired box 7, ventral anterior homeobox 1, sprouty RTK signaling antagonist 2, bone morphogenetic protein 4, and tropomyosin 1 genes were associated with higher risks of NSCL/P (P = 0.0001 to 0.04); 2 SNPs, 1 each in netrin 1 and V-maf avian musculoaponeurotic fibrosarcoma oncogene homolog B, were associated with a lower risk of NSCL/P (P = 0.013 to 0.03); and 2 SNPs, 1 each in ATP binding cassette subfamily A member 4 (ABCA4) and noggin, showed associations with NSCL/P that approached the threshold of significance (P = 0.056 to 0.07). In addition, 6 gene-gene interactions (P = 0.0001 to 0.001) and an ABCA4-folic acid consumption interaction (P < 0.0001) were identified. On the basis of these results, combined with those of previous association studies in the literature and biological characterizations of murine models, we propose an interaction network in which interferon regulatory factor 6 plays a central role in the etiology of NSCL/P.