Fine-mapping of 5q12.1-13.3 unveils new genetic contributors to caries.

Caries is a multifactorial disease and little is still known about the host genetic factors influencing susceptibility. Our previous genome-wide linkage scan has identified the interval 5q12.1-5q13.3 as linked to low caries susceptibility in Filipino families. Here we fine-mapped this region in order to identify genetic contributors to caries susceptibility. Four hundred and seventy-seven subjects from 72 pedigrees with similar cultural and behavioral habits and limited access to dental care living in the Philippines were studied. DMFT scores and genotype data of 75 single-nucleotide polymorphisms were evaluated in the Filipino families with the Family-Based Association Test. For replication purposes, a total 1,467 independent subjects from five different populations were analyzed in a case-control format. In the Filipino cohort, statistically significant and borderline associations were found between low caries experience and four genes spanning 13 million base pairs (PART1, ZSWIM6, CCNB1, and BTF3). We were able to replicate these results in some of the populations studied. We detected PART1 and BTF3 expression in whole saliva, and the expression of BTF3 was associated with caries experience. Our results suggest BTF3 may have a functional role in protecting against caries.

Association of AXIN2 with non-syndromic oral clefts in multiple populations.

We have previously shown the association of AXIN2 with oral clefts in a US population. Here, we expanded our study to explore the association of 11 AXIN2 markers in 682 cleft families from multiple populations. Alleles for each AXIN2 marker were tested for transmission distortion with clefts by means of the Family-based Association Test. We observed an association with SNP rs7224837 and all clefts in the combined populations (p = 0.001), and with SNP rs3923086 and cleft lip and palate in Asian populations (p = 0.004). We confirmed our association findings in an additional 528 cleft families from the United States (p < 0.009). We tested for gene-gene interaction between AXIN2 and additional cleft susceptibility loci. We assessed and detected Axin2 mRNA and protein expression during murine palatogenesis. In addition, we also observed co-localization of Axin2 with Irf6 proteins, particularly in the epithelium. Our results continue to support a role for AXIN2 in the etiology of human clefting. Additional studies should be performed to improve our understanding of the biological mechanisms linking AXIN2 to oral clefts.

Novel cleft susceptibility genes in chromosome 6q.

Cleft lip/palate is a defect of craniofacial development. In previous reports, chromosome 6q has been suggested as a candidate region for cleft lip/palate. A multipoint posterior probability of linkage analysis of multiplex families from the Philippines attributed an 88% probability of harboring a cleft-susceptibility gene to a narrower region on bands 6q14.2-14.3. We genotyped 2732 individuals from families and unrelated individuals with and without clefts to investigate the existence of possible cleft-susceptibility genes in this region. We found association of PRSS35 and SNAP91 genes with cleft lip/palate in the case-control cohort and in Caucasian families. Haplotype analyses support the individual associations with PRSS35. We found Prss35 expression in the head and palate of mouse embryos at critical stages for palatogenesis, whereas Snap91 was expressed in the adult brain. We provide further evidence of the involvement of chromosome 6q in cleft lip/palate and suggest PRSS35 as a novel candidate gene.

Reduced folate carrier 1 (RFC1) is associated with cleft of the lip only.

In this report, we have reanalyzed genotyping data in a collection of families from South America based on maternal origin. Genotyping analysis was performed at the Craniofacial Anomalies Research Center at the University of Iowa. These genotypes were derived from genomic DNA samples obtained from blood spots from children born with isolated orofacial clefts in 45 hospitals located in eight countries (Argentina, Bolivia, Brazil, Chile, Ecuador, Paraguay, Uruguay, and Venezuela) collaborating with ECLAMC (Latin American Collaborative Studies of Congenital Malformations) between January 1998 and December 1999. Dried blood samples were sent by regular mail to the Laboratory of Congenital Malformations, Federal University of Rio de Janeiro. Previous findings suggested that mitochondrial haplotype D is more commonly found among cleft cases born in South America. We hypothesized that association of certain genes may depend upon the ethnic origin, as defined by population-specific markers. Therefore, we tested if markers in MTHFR (5,10-methylenetetrahydrofolate reductase) and RFC1 (reduced folate carrier 1) were associated with oral clefts, depending on the maternal origin defined by the mitochondrial haplotype. Transmission distortion of alleles in MTHFR C677T and RFC1 G80A polymorphic variants was tested in 200 mother/affected child pairs taking into consideration maternal origin. RFC1 variation was over-transmitted to children born with cleft lip only (P = 0.017) carrying mitochondrial DNA haplotypes other than haplotype D. Our results provide a new indication that variation in RFC1 may contribute to cleft lip only. Future studies should investigate the association between oral clefts and RFC1 based on more discrete phenotypes.

Reduced folate carrier 1 (RFC1) is associated with cleft of the lip only

In this report, we have reanalyzed genotyping data in a collection of families from South America based on maternal origin. Genotyping analysis was performed at the Craniofacial Anomalies Research Center at the University of Iowa. These genotypes were derived from genomic DNA samples obtained from blood spots from children born with isolated orofacial clefts in 45 hospitals located in eight countries (Argentina, Bolivia, Brazil, Chile, Ecuador, Paraguay, Uruguay, and Venezuela) collaborating with ECLAMC (Latin American Collaborative Studies of Congenital Malformations) between January 1998 and December 1999. Dried blood samples were sent by regular mail to the Laboratory of Congenital Malformations, Federal University of Rio de Janeiro. Previous findings suggested that mitochondrial haplotype D is more commonly found among cleft cases born in South America. We hypothesized that association of certain genes may depend upon the ethnic origin, as defined by population-specific markers. Therefore, we tested if markers in MTHFR (5,10-methylenetetrahydrofolate reductase) and RFC1 (reduced folate carrier 1) were associated with oral clefts, depending on the maternal origin defined by the mitochondrial haplotype. Transmission distortion of alleles in MTHFR C677T and RFC1 G80A polymorphic variants was tested in 200 mother/affected child pairs taking into consideration maternal origin. RFC1 variation was over-transmitted to children born with cleft lip only (P = 0.017) carrying mitochondrial DNA haplotypes other than haplotype D. Our results provide a new indication that variation in RFC1 may contribute to cleft lip only. Future studies should investigate the association between oral clefts and RFC1 based on more discrete phenotypes.

Regional analysis on the occurrence of oral clefts in South America.

The aim of this work was to search for unequal birth prevalence rates (BPRs) of cleft lip +/- cleft palate (CL/P), and cleft palate only (CPO), among different geographic areas in South America, and to analyze phenotypic characteristics and associated risk factors in each identified cluster. Included were 5,128 CL/P cases, 1,745 CPO cases, and 3,712 controls (like-sexed, non-malformed liveborn infant, born immediately after a malformed one, in the same hospital), over 4,199,630 consecutive births. They were ascertained between 1967 and 2004, in 190 maternity hospitals of the ECLAMC (Estudio Colaborativo Latinoamericano de Malformaciones Congénitas) network, in 102 cities of all 10 South American countries. Non-predefined geographical areas with significantly unusual cleft BPRs were identified with Kulldorf and Nagarwalla's spatial scan statistic, employing number of cases and births, and exact location of each hospital. Expected values were cleft BPRs registered for the entire ECLAMC hospital network. Syndromic and non-syndromic clefts were considered for cluster analysis, and phenotypic characterization, while only non-syndromic for risk factor analysis. Seven clusters for CL/P, and four for CPO, with unusual BPRs were identified. CL/P cases in high BPR areas were more severe than elsewhere in the sample, similar to a previous ECLAMC report on microtia. For CL/P, high BPR clusters were associated with high altitude above sea level, Amerindian ancestry, and low socioeconomic strata; low BPR clusters showed association with African Black ancestry. Advanced maternal age, a recognized risk factor for CPO, was also associated with the only identified geographic cluster for CPO.

Genetic evidence for the role of loci at 19q13 in cleft lip and palate.

BACKGROUND: Clefts of the lip and palate are common birth defects, affecting approximately 1 in 700 births worldwide. The aetiology of clefting is complex, with multiple genetic and environmental influences. METHODS: Genotype based linkage disequilibrium analysis was conducted using the family based association test (FBAT) and the likelihood ratio test (LRT). We also carried out direct sequencing of the PVR and PVRL2 candidate genes based on their homology to PVRL1, a gene shown previously to cause Margarita Island clefting. Participants included 434 patients with cleft lip with or without cleft palate or cleft palate only and their mothers from eight countries in South America, 205 nuclear triads (father-mother-affected child) from Iowa, 541 nuclear triads from Denmark, and 100 patients with cleft lip and palate from the Philippines. RESULTS: An allelic variant in the PVR gene showed statistically significant association with both South American and Iowa populations (p = 0.0007 and p = 0.0009, respectively). Direct sequencing of PVR and PVRL2 yielded 26 variants, including two rare amino acid changes, one in each gene, which were not seen in controls. CONCLUSIONS: We found an association between a common variant in a gene at 19q and isolated clefting in two heterogeneous populations. However, it is unclear from our data if rare variants in PVR and PVRL2 are sufficient to cause clefting in isolation.

Complete sequencing shows a role for MSX1 in non-syndromic cleft lip and palate.

MSX1 has been proposed as a gene in which mutations may contribute to non-syndromic forms of cleft lip and/or cleft palate. Support for this comes from human linkage and linkage disequilibrium studies, chromosomal deletions resulting in haploinsufficiency, a large family with a stop codon mutation that includes clefting as a phenotype, and the Msx1 phenotype in a knockout mouse. This report describes a population based scan for mutations encompassing the sense and antisense transcribed sequence of MSX1 (two exons, one intron). We compare the completed genomic sequence of MSX1 to the mouse Msx1 sequence to identify non-coding homology regions, and sequence highly conserved elements. The samples studied were drawn from a panethnic collection including people of European, Asian, and native South American ancestry. The gene was sequenced in 917 people and potentially aetiological mutations were identified in 16. These included missense mutations in conserved amino acids and point mutations in conserved regions not identified in any of 500 controls sequenced. Five different missense mutations in seven unrelated subjects with clefting are described. Evolutionary sequence comparisons of all known Msx1 orthologues placed the amino acid substitutions in context. Four rare mutations were found in non-coding regions that are highly conserved and disrupt probable regulatory regions. In addition, a panel of 18 population specific polymorphic variants were identified that will be useful in future haplotype analyses of MSX1. MSX1 mutations are found in 2% of cases of clefting and should be considered for genetic counselling implications, particularly in those families in which autosomal dominant inheritance patterns or dental anomalies appear to be cosegregating with the clefting phenotype.

Inheritance of cleft palate in South America: evidence for a major locus recessive.

OBJECTIVES: Determine the model of inheritance of non-syndromic cleft palate in humans. DESIGN: Complex segregation analysis performed in families of consecutive newborns affected with non-syndromic cleft palate. SETTING AND SAMPLE POPULATION: The Latin American Collaborative Study of Congenital Malformations (ECLAMC). Four hundred and seven consecutive newborns affected with non-syndromic cleft palate registered during the period 1967-97. OUTCOME MEASURE: Likelihood ratio test and Akaike information criterion (AIC) values. RESULTS: The single major locus recessive model provided a significantly better explanation of the data. It was the most parsimonious and had the smallest AIC value of the six models tested with approximately the same likelihood as the general model (chi2 = 2.44, p = 0.5). CONCLUSIONS: To have defined a genetic model for non-syndromic cleft palate and provided evidence for a single major locus inheritance suggests that genetic linkage studies could be implemented.

MSX1 and TGFB3 contribute to clefting in South America.

MSX1 and TGFB3 have been proposed as genes in which mutations may contribute to non-syndromic forms of oral clefts; however, an interaction between these genes has not been described. The present study attempts to detect transmission distortion of MSX1 and TGFB3 in 217 South American children from their respective mothers. With transmission disequilibrium test analysis, cleft lip with/without cleft palate, cleft lip with palate plus cleft palate only, and all datasets combined showed evidence of association with MSX1 (p = 0.004, p = 0.037, and p = 0.001, respectively). With likelihood ratio test analysis, "cleft lip only" showed association with MSX1 (p = 0.04) and "cleft palate only" with TGFB3 (p = 0.02). A joint analysis of MSX1 and TGFB3 suggested that there may be an interaction between these two loci to increase cleft susceptibility. These results suggest that MSX1 and TGFB3 mutations make a contribution to clefts in South American populations.

Genetic origins in a South American clefting population.

It has been proposed that susceptibility to clefting in South America is related to Amerindian ancestry, where clefting is present at a higher frequency than in the other admixed populations (Caucasian and African) that make up the diverse racial mix of current South Americans. To clarify the genetic origins and establish a method for genetic mapping, mitochondrial DNA variation and Y-chromosome markers were studied in a South American population affected with clefting. Two-hundred and seventeen subjects and matched controls were selected through the Latin-American Collaborative Study of Congenital Malformations (ECLAMC). The case group showed a higher frequency of Native American haplogroups and a lower frequency of African haplogroups (p < 0.00001). In addition, the case group showed a much higher frequency of the specific native American haplogroup D than the control group (p < 0.00001). For the Y-chromosome markers, the case group showed a lower frequency of the African-specific marker, YAP (p = 0.002), and a higher frequency of the Native American-specific marker, DYS199 (p < 0.00001). Even though differences were found in the frequencies of the markers studied, the contribution of each founder population was similar for both groups. Results suggest a strong Native American maternal contribution and a strong Caucasian (Spanish and Portuguese) paternal contribution to the population studied. The implications of this finding include the possibility of using admixture mapping approaches to this population.

Identification of novel mutations in SHH and ZIC2 in a South American (ECLAMC) population with holoprosencephaly.

Holoprosencephaly (HPE) is genetically heterogeneous with four genes, SIX3, SHH, TGIF, and ZIC2 that have been identified to date and that are altered in 12% of patients. To analyze this prevalence in a South American population-based sample (57 HPE cases in 244,511 live and still births or 1 in 4300), we performed a mutational study of these genes in 30 unrelated children (26 newborns and 4 non-newborns) with HPE being ascertained by ECLAMC (Latin American Collaborative Study of Congenital Malformations). We identified three novel mutations: two were missense mutations of the SHH gene (Cys183-->Phe; His140-->Pro); the third mutation was a 2-bp deletion in the zinc-finger region of the ZIC2 gene. These molecular results explained 8% (2/26 newborn samples) of the HPE cases in this South American population-based sample, a proportion similar to our previously published data from a collection of cases.

Correlation between molecular and conventional genealogies in Aicuña: a rural population from Northwestern Argentina.

Aicuña is a village in the northwest of Argentina, located about 300 km south of La Rioja city, in the province of La Rioja. The population of Aicuña derives from a founder couple established in the uninhabited Aicuña valley in the early years of the 17th century. Due to land ownership litigation, the descendants maintained a well-documented genealogy that extends for 12 generations, comprising more than 8,000 individuals. From the historical pedigree of Aicuña, we selected 14 males with direct patrilineal descent from the 2 most ancient male founders, and 23 donors (9 females and 14 males) with direct matrilineal descent from the most ancient female founder. All 3 founders lived in the 17th century. We collected DNA from buccal swabs and characterized the mitochondrial DNA (mtDNA) and Y haplotypes using 14 Y-specific markers, 11 mtDNA polymorphic markers and sequencing of the mt hypervariable regions 1 and 2. We found four different Y haplotypes: Y1 and Y2 haplotypes of European origin corresponding to the founder ancestors Francisco Páez de Espinoza and Apolinario Ormeño, which were shared by 6 and 3 donors, respectively. Three males selected as Ormeño patrilineal descendants showed a different Y haplotype (Y3), probably originated by erroneous paternity registration due to illegitimacy. The remaining case (haplotype Y4), also assumed to belong to the Ormeño lineage, was probably also due to an erroneously registered paternity. Twenty-two donors showed an association of mtDNA markers corresponding to the Amerindian haplotype A2. The founder of this matrilineage could be traced back for more than 14 generations. The haplotype B of one remaining female did not correspond with the historical pedigree and could be due to an error in the genealogy registration. Our results showed an 85% agreement between conventional and molecular genealogies, with mtDNA markers being Amerindian, and Y markers being European. The methodology used in this report is a tool which could potentially be employed as a precedent for land ownership by Aicuña villagers and Amerindian populations.

Candidate genes for nonsyndromic cleft lip and palate.

The confirmation of supposed genes causing susceptibility to nonsyndromic cleft lip with or without a cleft palate (CL/P) and cleft palate alone (CP) would help to understand the molecular development of the lip, the palate and the jaw, and to predict more accurately the risk of recurrence of such defects. The purpose of this article is to present a brief review of the current state of knowledge regarding the search for genes responsible for the occurrence of CL/P and CP. After ten years of research, approximately twenty candidate genes have already been suggested for CL/P and CP. Some genes or chromosomal regions seem to be frequently associated with these defects and a specific nomenclature (orofacial cleft genes--OFC) has been suggested. Everything indicates that it will still take many years of research before the genes responsible for CL/P and CP are confirmed. These efforts are justified, however, because of the possibility of being able to predict more accurately the risk of such defects occurring.

Isolated small intestinal atresias in Latin America and Spain: epidemiological analysis.

Stenosis, atresia, or absence of part of the duodenum, jejunum, or ileum are generally considered small intestinal atresias (SIAs). SIAs occur as isolated defects, in combination with other unrelated congenital anomalies, or as part of syndromes. We performed an epidemiological study of infants with isolated SIAs using data from two large congenital defects registries, one from Latin America (ECLAMC) and the other from Spain (ECEMC). The overall prevalence of SIAs is similar in both programs, being 1.32 per 10,000 livebirths in Spain and 1.29 per 10.000 livebirths in Latin America. Our results suggest that infants with isolated SIAs are characterized epidemiologically on the basis of shorter gestational age and low birthweight, an association with twinning, the parents are more frequently consanguineous, and their pregnancies are more frequently complicated by vaginal bleeding. The results also suggest an association between some maternal infections and ileal atresia. The fact that these characteristics have been observed in children with these types of anomalies occurring in different geographical areas and populations supports the conclusion that these characteristics are causally related to these defects.

Epidemiological assessment of misoprostol teratogenicity.

OBJECTIVE: To verify if any of the 15 congenital defects already reported in association with misoprostol can be found within an epidemiological registry of congenital defects. DESIGN: Case-control study including case-sick and case-health controls. METHODS: Comparison of misoprostol exposure for each specific defect, using the exposure for the rest of defects as a reference group. POPULATION: Four thousand six hundred seventy-three consecutive newborn infants with malformations of unknown aetiology, in the Latin American Collaborative Study of Congenital Malformation. RESULTS: There was no difference in exposure rate between the malformed (34/4,673) and nonmalformed (23/4,980) newborns. Four of the five more frequently cited defects in the literature were found to be in excess: constriction ring, terminal transverse-limb defects, hydrocephalus, and arthrogryposis. Equinovarus feet had a normal frequency in our study. Thirteen different defects not described in the literature were seen in our misoprostol exposed cases, but only holoprosencephaly and bladder exstrophy significantly exceeded the expected number. CONCLUSIONS: The confirmation from an epidemiological registry of an association for four of the five more commonly observed congenital defects among misoprostol exposed children described in the literature seems indicative of a real teratogenic effect. The defects are of vascular disruption type. However, additional attempts to achieve abortion could not be excluded as a concurrent contribution.

Thumb/hallux duplication and preaxial polydactyly type I.

It was recently shown that hand postaxial polydactyly differed from foot postaxial polydactyly. The aim of this work was to test whether thumb and hallux duplication also had different clinical and epidemiological characteristics, depending on limb involvement. We studied 920 newborn infants with first digit duplication, ascertained among 3,444,374 births by the Latin-American Collaborative Study of Congenital Malformations (ECLAMC), from 1967 to 1995. Since biphalangeal thumb duplication or hallux duplication can occur in families with triphalangeal thumb or polysyndactylous propositi, these groups were also analyzed. The 715 isolated (nonsyndromal) cases (prevalence 2.08 per 10,000) were subdivided into five groups: thumb duplication (N = 568; prevalence: 1.65/10,000); hallux duplication (N = 82; prevalence: 0.24); thumb and/or hallux duplication plus syndactyly (polysyndactyly) (N = 37; prevalence: 0.11); triphalangeal thumb (N = 24; prevalence: 0.07), and thumb duplication plus hallux duplication (N = 4; prevalence: 0.01). Both thumb and hallux duplication groups showed a significant excess of males, and right sidedness was also more frequent in both of them, though without statistical significance for hallux duplication. Thumb duplication was more often unilateral (94.7% versus hallux duplication of 81.5%), and its prevalence was higher in Bolivia (3.37/10,000) than in the other 10 Latin-American countries included (1.62/10,000). In a subseries of 405 preaxial polydactylies with matched controls, a logistic regression analysis showed that birth weight and gestational age had an effect on the calculated risk of having an infant with thumb duplication, while first trimester vaginal bleeding had only a borderline effect. None of the polydactyly groups showed abnormal values for twinning, perinatal mortality, ethnicity, maternal education, parental ages, parity, parental subfertility, or consanguinity. There were 70/405 familial cases. Their pedigrees were compatible with autosomal dominant inheritance with a 9% penetrance for thumb duplication and hallux duplication and a 70% penetrance for triphalangeal thumb and polysyndactyly. Inheritance of thumb duplication and probably the untested inheritance of hallux duplication were also compatible with a four-locus multiplicative model. The observed differences in laterality, geographical distribution, birth weight, gestational age, and first trimester vaginal bleeding between thumb duplication and hallux duplication groups suggested that apparent preaxial polydactyly type 1 is a causally heterogeneous group.

Pregnancy outcome after exposure to misoprostol in Brazil: a prospective, controlled study.

BACKGROUND: Misoprostol, a synthetic prostaglandin E1 analog is labeled for the treatment of gastric and duodenal ulcers. In Brazil, where abortion is not a legal procedure, there is a widespread popular misuse of this drug in abortion attempts. This misuse and the fact that, in many cases the desired pregnancy termination does not occur, raise concerns about fetal safety. Case reports of congenital anomalies after maternal use of misoprostol have been published. The objective of this work was to compare pregnancy outcome following misoprostol exposure with a matched control group. This is the first prospective controlled study on fetal safety after misoprostol use. METHODS: A prospective, observational cohort study with 86 exposed and 86 pair-matched, non-exposed controls. RESULTS: There was no significant difference in the rates of major or minor birth between exposed compared to non-exposed infants (2/67 vs 2/81, major defects; 7/67 vs. 3/81, minor anomalies) There were significantly more miscarriages in the exposed group (17.1% vs. 5.8%; relative risk, 2.97; 95% confidence interval, 1.12 to 7.88). There was no statistical difference in gestational age at delivery, birth weight, sex ratio, rate of prematurity, low birth weight, or rates of cesarean section between groups. CONCLUSIONS: Our study, despite its limited statistical power, does not suggest a potent teratogenic action of misoprostol exposure during pregnancy.

Survival of children with Down syndrome in South America. ECLAMC-Downsurv Group. Latin American Collaborative Study of Congenital Malformations.

The first step of all healthcare actions aimed at promoting an appropriate quality of life for infants affected by Down syndrome (DS) is to ensure their survival. This investigation was aimed at estimating the infant mortality rate of infants affected with DS in urban populations of South America. Thirty-three hospitals included in the Latin American Collaborative Study of Congenital Malformations (ECLAMC) distributed in 23 cities of 5 South American countries followed 360 liveborn DS cases born during the 1988-1992 period. Families were recontacted after the infant should have reached the age of one year. The collected data included information about health status; i.e., frequency and dates of diagnosed illnesses and hospital admissions, and, in case of death, information on date, place and cause of death, and illness immediately before death. Information about the interviews included place, date, and name of the interviewer. A closed questionnaire was employed by the interviewers, mostly physicians, nurses, and social workers. Life table analysis up to the age of one year was performed by the actuarial survival method. The overall mean survival at age one year was 0.736 (SE=0.023). Thirty-three (9.2%) of the 360 cases died neonatally, and 62 (17.2%) within the remaining 2-to-12-month interval. The probability of survival at one year of age did not differ between public (209 cases; mean 0.718; SE=0.031) and private (151 cases; mean: 0.762; SE=0.035) (chi2:0.87; df:1; P >0.05) health systems. The 150 DS cases with a congenital heart defect (CHD) had a significantly lower P robability of survival at the age of one year (mean: 0.660; SE: 0.039) than did the 210 cases without CHD (mean: 0.790; SE: 0.028) (chi2:6.67; df:1; P <0.01). The death rate in the first year of life for DS cases without a detected cardiac defect (21%) is significantly higher than that reported in developed countries; namely, 16% from Italy, 11% from Canada, 10% from England, and 7% from Denmark.