Whole genome sequencing of a family with autosomal dominant features within the oculoauriculovertebral spectrum.

Background: Oculoauriculovertebral Spectrum (OAVS) encompasses a wide variety of anomalies on derivatives from the first and second pharyngeal arches including macrostomia, hemifacial microsomia, micrognathia, preauricular tags, ocular and vertebral anomalies. We present the genetic findings of a large three-generation family with multiple members affected with macrostomia, preauricular tags and uni- or bilateral ptosis following an autosomal dominant segregation pattern. Methods: We generated whole genome sequencing data for the proband, affected parent and unaffected paternal grandparent followed by Sanger sequencing on 23 family members for the top 10 candidate genes: KCND2, PDGFRA, CASP9, NCOA3, WNT10A, SIX1, MTF1, KDR/VEGFR2, LRRK1, and TRIM2. We performed parent and sibling-based transmission disequilibrium tests and burden analysis to explore segregation and burden of candidate gene mutations. Bioinformatic analyses investigated the biological connection between genes and the abnormal phenotypes. Results: Overall, rare missense mutations in SIX1, KDR/VEGFR2, and PDGFRA showed the best evidence of segregation with the OAV phenotypes in this family. When considering affection with any of the 3 OAVS phenotypes as an outcome, parent-TDTs and sib-TDTs (unadjusted p-values) found that SIX1 (p=0.025, p=0.052), followed by PDGFRA (p=0.180, p=0.069) and KDR/VEGFR2 (p=0.180, p=0.069) have the strongest associations in this family. Burden analysis via a penalized linear mixed model identified SIX1 (RC=0.87) and PDGFRA (RC=0.98) as having the strongest association with OAVS severity. Using phenotype-specific ogfrautcomes, sib-TDTs identified associations between (1) SIX1 with uni- or bilateral ptosis (p=0.049) and ear tags (p=0.01), (2) PDGFRA and KDR/VEGFR2 with ear tags (both p<0.01). Conclusion: Our study reports the genomic findings of a large family with multiple individuals affected with OAVS phenotypes with autosomal dominant inheritance. Our findings narrow down to three potential candidate genes, SIX1, PDGFRA, and KDR/VEGFR2. Among these, SIX1 has been previously associated with OAVS ear malformations and it is co-expressed with EYA1 during ear development. Attempts to strengthen the genotype-phenotype co-relation underlying the OAVS of phenotypes are essential to discover the etiological factors leading to this complex and burdensome condition as well as for family counseling and prevention efforts.

DNA methylation differences in monozygotic twins with Van der Woude syndrome.

Introduction: Van der Woude Syndrome (VWS) is an autosomal dominant disorder responsible for 2% of all syndromic orofacial clefts (OFCs) with IRF6 being the primary causal gene (70%). Cases may present with lip pits and either cleft lip, cleft lip with cleft palate, or cleft palate, with marked phenotypic discordance even among individuals carrying the same mutation. This suggests that genetic or epigenetic modifiers may play additional roles in the syndrome's etiology and variability in expression. We report the first DNA methylation profiling of 2 pairs of monozygotic twins with VWS. Our goal is to explore epigenetic contributions to VWS etiology and variable phenotypic expressivity by comparing DNAm profiles in both twin pairs. While the mutations that cause VWS in these twins are known, the additional mechanism behind their phenotypic risk and variability in expression remains unclear. Methods: We generated whole genome DNAm data for both twin pairs. Differentially methylated positions (DMPs) were selected based on: (1) a coefficient of variation in DNAm levels in unaffected individuals < 20%, and (2) intra-twin pair absolute difference in DNAm levels >5% (delta beta > | 0.05|). We then divided the DMPs in two subgroups for each twin pair for further analysis: (1) higher methylation levels in twin A (Twin A > Twin B); and (2) higher methylation levels in twin B (Twin B >Twin A). Results and Discussion: Gene ontology analysis revealed a list of enriched genes that showed significant differential DNAm, including clef-associated genes. Among the cleft-associated genes, TP63 was the most significant hit (p=7.82E-12). Both twin pairs presented differential DNAm levels in CpG sites in/near TP63 (Twin 1A > Twin 1B and Twin 2A < Twin 2B). The genes TP63 and IRF6 function in a biological regulatory loop to coordinate epithelial proliferation and differentiation in a process that is critical for palatal fusion. The effects of the causal mutations in IRF6 can be further impacted by epigenetic dysregulation of IRF6 itself, or genes in its pathway. Our data shows evidence that changes in DNAm is a plausible mechanism that can lead to markedly distinct phenotypes, even among individuals carrying the same mutation.

Genome-wide Gene-by-Sex Interaction Studies Identify Novel Nonsyndromic Orofacial Clefts Risk Locus.

Risk loci identified through genome-wide association studies have explained about 25% of the phenotypic variations in nonsyndromic orofacial clefts (nsOFCs) on the liability scale. Despite the notable sex differences in the incidences of the different cleft types, investigation of loci for sex-specific effects has been understudied. To explore the sex-specific effects in genetic etiology of nsOFCs, we conducted a genome-wide gene × sex (GxSex) interaction study in a sub-Saharan African orofacial cleft cohort. The sample included 1,019 nonsyndromic orofacial cleft cases (814 cleft lip with or without cleft palate and 205 cleft palate only) and 2,159 controls recruited from 3 sites (Ethiopia, Ghana, and Nigeria). An additive logistic model was used to examine the joint effects of the genotype and GxSex interaction. Furthermore, we examined loci with suggestive significance (P < 1E-5) in the additive model for the effect of the GxSex interaction only. We identified a novel risk locus on chromosome 8p22 with genome-wide significant joint and GxSex interaction effects (rs2720555, p2df = 1.16E-08, pGxSex = 1.49E-09, odds ratio [OR] = 0.44, 95% CI = 0.34 to 0.57). For males, the risk of cleft lip with or without cleft palate at this locus decreases with additional copies of the minor allele (p < 0.0001, OR = 0.60, 95% CI = 0.48 to 0.74), but the effect is reversed for females (p = 0.0004, OR = 1.36, 95% CI = 1.15 to 1.60). We replicated the female-specific effect of this locus in an independent cohort (p = 0.037, OR = 1.30, 95% CI = 1.02 to 1.65), but no significant effect was found for the males (p = 0.29, OR = 0.86, 95% CI = 0.65 to 1.14). This locus is in topologically associating domain with craniofacially expressed and enriched genes during embryonic development. Rare coding mutations of some of these genes were identified in nsOFC cohorts through whole exome sequencing analysis. Our study is additional proof that genome-wide GxSex interaction analysis provides an opportunity for novel findings of loci and genes that contribute to the risk of nsOFCs.

[MFN2 gene analysis in patients with hereditary motor and sensory neuropathy from Bashkortostan Republic].

Hereditary motor and sensory neuropathy (HMSN) type IIA is caused by mutations in the mitofusin type-2 (MFN2) gene and represents one of the most common axonal forms of HMSN. We determined the spectrum and frequency of MFN2 gene mutations in patients from the Bashkortostan Republic (BR). Four different mutations were revealed in 5 out of 170 unrelated patients, i.e., c.2113G>A (p.Val705Ile) (1.2% among all types of H MSN in the total sample of patients and 2% among patients of Tatar ethnicity). This mutation was described previously; c.775C>T (p.Arg259Cys) (0.6%, in the total sample of patients and 2% among the patients of Tatar ethnicity); c.776G>A (p.Arg259His) (0.6% in the total sample of patients and 1.5% among the patients of Russians ethnicity); and c.2171T>C (p.Leu724Pro) (1.2% in the total sample of patients and 7.4% among the patients of Bashkirs ethnicity). These are new mutations that were not observed among healthy family members and in control samples of healthy subjects. Five identified nucleotide substitutions represent single nucleotide polymorphisms of the gene, including c.892G>A (p.Gly298Arg), c.957C>T (Gly319Gly), and c1039-222t>c, which were described previously, while c.175+28c>t and c.2204+15t>c represent new nucleotide substitutions in the intron regions of the gene.

[Genetic epidemiological study of monogenic hereditary diseases in the Republic of Tatarstan: population dynamic factors determining the differentiation of the load of hereditary diseases in five districts].

A genetic epidemiological study has been performed in five districts of the Republic of Tatarstan, Russia: Arsky, Atninsky, Kukmorsky, Buinsky and Drozhzhanovsky raions. The total size of the population surveyed is 188 397 people. Tatars accounted for 77.13% of the population analyzed (145466 people) and were represented by two main ethnic groups: Kazan Tatars and Mishars. The medical genetic study encompassed the total population of the districts, irrespective of ethnicity, and was carried out according to the standard protocol developed in the Laboratory of Genetic Epidemiology of the Research Center for Medical Genetics of the Russian Academy of Medical Sciences. After segregation analysis, the prevalence rates of the main types of monogenic hereditary disorders (MHDs), i.e., autosomal dominant (AD), autosomal recessive (AR), and X-linked diseases, have been calculated for the total population of the five districts and for Tatars alone. The prevalence rates ofAD, AR, and X-linked diseases considerably vary in different subpopulations. The largest difference in the MHD prevalence rate has been found between the rural and urban populations. The overall prevalence rate of MHDs was one patient per 293 urban residents and populations and one patient per 134 rural residents, with a wide variation between subpopulations, from 1 : 83 people in the rural population of Atninsky raion to 1: 351 people in the town of Kukmor. Comparison of the MHD prevalence rate in Tatars with those in populations surveyed earlier has shown that the characteristics of the load of MHDs in the Tatar population are similar to those in some districts of the republics of Bashkortostan, Udmurtia, Mari El, and Chuvachia. In Russian populations of European Russia, the MHD prevalence rates are substantially lower. Correlation analysis has shown high (r = 0.5-0.9) significant correlations between the local inbreeding (a), the im index, the random inbreeding (F(ST)), and the AD and AR prevalence rates in the Tatar population. This analysis has demonstrated that genetic drift is the main population dynamic factor determining the MHD load in the Tatar population.

Clinical findings in patients with GLI2 mutations--phenotypic variability.

Mutations in the human GLI2 gene were first reported in association with defective anterior pituitary formation, panhypopituitarism, and forebrain anomalies represented by typical holoprosencephaly (HPE) and holoprosencephaly-like (HPE-L) phenotypes and postaxial polydactyly. Subsequently, anophthalmia plus orbital anomalies, heminasal aplasia, branchial arch anomalies and polydactyly have also been incorporated into the general phenotype. Here we described six Brazilian patients with phenotypic manifestations that range from isolated cleft lip/palate with polydactyly, branchial arch anomalies to semi-lobar holoprosencephaly. Novel sequence variants were found in the GLI2 gene in patients with marked involvement of the temporomandibular joint (TMJ), a new clinical finding observed with mutations of this gene. Clinical, molecular and genetic aspects are discussed.

Genetic studies in the Nigerian population implicate an MSX1 mutation in complex oral facial clefting disorders.

BACKGROUND: Orofacial clefts are the most common malformations of the head and neck, with a worldwide prevalence of 1 in 700 births. They are commonly divided into CL(P) and CP based on anatomic, genetic, and embryologic findings. A Nigerian craniofacial anomalies study (NigeriaCRAN) was set up in 2006 to investigate the role of gene-environment interaction in the origin of orofacial clefts in Nigeria. SUBJECTS AND METHODS: DNA isolated from saliva from Nigerian probands was used for genotype association studies and direct sequencing of cleft candidate genes: MSX1 , IRF6 , FOXE1, FGFR1 , FGFR2 , BMP4 , MAFB, ABCA4 , PAX7, and VAX1 , and the chromosome 8q region. RESULTS: A missense mutation A34G in MSX1 was observed in nine cases and four HapMap controls. No other apparent causative variations were identified. Deviation from Hardy Weinberg equilibrium (HWE) was observed in these cases (p = .00002). A significant difference was noted between the affected side for unilateral CL (p = .03) and bilateral clefts and between clefts on either side (p = .02). A significant gender difference was also observed for CP (p = .008). CONCLUSIONS: Replication of a mutation previously implicated in other populations suggests a role for the MSX1 A34G variant in the development of CL(P).

Association of cytokine gene alleles with the inflammation of human periodontal tissue.

Gingivitis and periodontitis are chronic inflammatory diseases of the periodontal tissue in humans caused by both environmental and genetic factors. The human cytokine genes that regulate the immune response may play an important role in the development of these chronic inflammatory diseases. The aim of this study is to analyze the allele status of eight human cytokine genes and to associate it with the inflammation of periodontal tissue in humans. A total of 296 unrelated males of Russian origin were studied. A significant association of theIL1BandIL6 minor alleles and gingivitis was found. In addition, we found a significant association of the OHI-S index with theIL18gene alleles. The influence of genetic factors on gingivitis may contribute to the understanding of the mechanisms of interaction between genetic and environmental factors in periodontal conditions, and to the identification of risk groups for effective prevention and treatment.

A new variant of Charcot-Marie-Tooth disease type 2 is probably the result of a mutation in the neurofilament-light gene.

Charcot-Marie-Tooth (CMT) disease is the most common inherited motor and sensory neuropathy. The axonal form of the disease is designated as "CMT type 2" (CMT2). Although four loci known to be implicated in autosomal dominant CMT2 have been mapped thus far (on 1p35-p36, 3q13. 1, 3q13-q22, and 7p14), no one causative gene is yet known. A large Russian family with CMT2 was found in the Mordovian Republic (Russia). Affected members had the typical CMT2 phenotype. Additionally, several patients suffered from hyperkeratosis, although the association, if any, between the two disorders is not clear. Linkage with the CMT loci already known (CMT1A, CMT1B, CMT2A, CMT2B, CMT2D, and a number of other CMT-related loci) was excluded. Genomewide screening pinpointed the disease locus in this family to chromosome 8p21, within a 16-cM interval between markers D8S136 and D8S1769. A maximum two-point LOD score of 5.93 was yielded by a microsatellite from the 5' region of the neurofilament-light gene (NF-L). Neurofilament proteins play an important role in axonal structure and are implicated in several neuronal disorders. Screening of affected family members for mutations in the NF-L gene and in the tightly linked neurofilament-medium gene (NF-M) revealed the only DNA alteration linked with the disease: a A998C transversion in the first exon of NF-L, which converts a conserved Gln333 amino acid to proline. This alteration was not found in 180 normal chromosomes. Twenty unrelated CMT2 patients, as well as 26 others with an undetermined form of CMT, also were screened for mutations in NF-L, but no additional mutations were found. It is suggested that Gln333Pro represents a rare disease-causing mutation, which results in the CMT2 phenotype.

[Hereditary nervous system diseases in Mordovia]. / Nasledstvennye bolezni nervnoi sistemy v Mordovii.

A medical genetic study on hereditary neural diseases was performed in 21 districts of the Mordovian Republic. The total number of persons examined was 936,800. The population load of autosomal dominant, autosomal recessive, and X-linked recessive diseases was 0.1696 +/- 0.0129, 0.1075 +/- 0.0107, and 0.0341 +/- 0.0010, respectively. Twenty-eight disease entities were revealed, including 10 autosomal recessive (AR), 15 autosomal dominant (AD), 2 X-linked recessive (XR) diseases, and 1 genetically heterogenous disease. These diseases were nonuniformly distributed among different populations of Mordovia. The incidence of AR diseases was highest in the Mordovian and Tatar populations; that of AD diseases, in the Russian population; and that of XR diseases, in the Mordovian population.

[Genetic structure and the load of hereditary diseases in five populations of Arkhangel'skaia region]. / Geneticheskaia struktura i gruz nasledstvennykh boleznei v piati populiatsiiakh Arkhangel'skoi oblasti.

A population and medical genetic investigation was performed in a number of raions in the Arkhangel' skaya oblast. Random inbreeding coefficients were 0.000358 and 0.000361 in the Vinogradovskii and Krasnoborskii raions. Malecot's local inbreeding coefficients were 0.000565 and 0.000472, respectively. The endogamy indices were 0.37 and 0.54, respectively. In the urban population, the loads of autosomal dominant, autosomal recessive, and X-linked pathology were 1.01 and 0.98 per 1000 individuals, and 0.29 per 1000 men; in the rural population, they were 1.22, 1.55, and 1.08, respectively. In the populations studied, the hereditary pathology spectrum is described.

Linkage of polymorphic congenital cataract to the gamma-crystallin gene locus on human chromosome 2q33-35.

Cataract is one of the major causes of blindness in humans. We describe here an autosomal dominant polymorphic congenital cataract (PCC) which is characterised by wide variations in phenotype of non-nuclear lens opacities, even among affected members of the same family. PCC families included a large, unique pedigree (254 members, 103 affected individuals), and genetic linkage was conducted using a variety of polymorphic markers. Evidence for linkage was found for chromosome 2q33-35 with PCC mapping near D2S72 and TNP1. A tri-nucleotide microsatellite marker for gamma-crystallin B gene (CRYG1) was found to co-segregate with PCC and yielded a maximum lod score of 10.62 at (theta = 0). A multipoint analysis demonstrated that the most probable location of the PCC gene was within an 8 cM genetic interval containing the gamma-crystallin gene cluster. These data provide strong evidence of the existence of an autosomal dominant mutation for PCC in or near the gamma-crystallin gene cluster. This defect is characterised by complete penetrance but variable expression of the cataract phenotype. Our study also suggests that non-nuclear human cataracts might be caused by some abnormality in gamma-crystallin genes.

[Genetic study of idiopathic torsion dystonia in Russia]. / Geneticheskoe izuchenie idiopaticheskoi torzionnoi distonii v Rossii.

Inheritance of idiopathic torsion dystonia (ITD) was studied in 41 Russian families including 41 probands with generalized, focal, and segmental dystonia and 140 recurred cases. Affected relatives appeared in two or more generations in 31 families analyzed. It was shown that in 76% of segregated cases, ITD was inherited as an autosomal dominant trait with a penetrance of 40% and varying expression. An autosomal recessive type was observed in 24% of the cases. Approximately 10% of the cases of disease could be caused by a new mutation and 14.6% by a nongenetic phenotype similar to genetic forms in its clinical symptoms. ITD with the X-linked recessive type of inheritance did not occur in the families studied. The recurrence risk was 20% in autosomal dominant forms. The risk correlated with age the relative's: clinical symptoms developed in 98.4% of patients by the age of 30.

[Population genetics of spinal muscular atrophy]. / Populiatsionnaia genetika spinal'nykh myshechnykh atrofii.

A population genetic study of spinal amyotrophy (SMA) in six Russian and three Central Asian regions was carried out. In total, 29 patients with autosomal recessive (AR) infantile proximal SMA (SMA I-III) and four patients with rare SMA forms with an unspecified type of inheritance were revealed. In Russian populations, the prevalence of SMA I-III is similar (1.5-2.5/100000), it is one of the most common hereditary neurological diseases. A tendency toward nonuniform territorial SMA prevalence is observed in genetically subdivided populations. The lesser SMA I-III prevalence in Central Asian populations might be due in part to inbreeding depression. A segregation frequency of 0.21 is in accordance with AR inheritance; the proportion of sporadic cases is 3%. Clinical genealogical data support the genetic unity of forms I-III. The origin of pedigrees with SMA in distant relatives is discussed.

[Hereditary spastic paraplegias: a comparative study of Russian populations]. / Nasledstvennye spasticheskie paraplegii: svranitel'noe issledovanie rossiiskikh populiatsii.

15 families (27 patients) with hereditary spastic paraplegia (HSP) were found in the course of monogenic disorders investigation in 6 Russian populations. High HSP prevalence (7.21+1.61) x 10(-5) was found in Kirov Province [the frequency of the gene of autosomal-dominant form was (3.61 +/- 1.14) x 10(-5), autosomal-recessive-(64.5 +/- 9.74)- 10(-6)]. The pronounced interfamilial polymorphism of HSP was observed. Two families with rare autosomal-recessive variation of "clear" HSP as well as two families with HSP associated with peroneal amyotrophies were revealed. Accumulation of cases with unusual combination of autosomal-dominant HSP together with mental deficiency was remarkable in Kirov Province.

Emery-Dreifuss syndrome: genetic and clinical varieties.

Two familial and 2 sporadic cases of Emery-Dreifuss syndrome are reported. One family presented a rare autosomal dominant variant of Emery-Dreifuss muscular dystrophy, another with X-linked recessive inheritance showed unusual intrafamilial variability. One of sporadic cases closely resembled rigid spine syndrome, the other was clinically intermediate between Emery-Dreifuss muscular dystrophy and rigid spine syndrome, showing that they are not distinct disorders.

[Population genetic study of hereditary motor and sensory neuropathy in the Kirov region]. / Populiatsionno-geneticheskoe issledovanie nasledstvennoi motorno-sensornoi nevropatii v kirovskoi oblasti.

All the cases of hereditary motor and sensory neuropathy (HMSN) in an eastern part of Kirov region (Russian north-east) were ascertained (N = 42 including 11 persons with pre/subclinical forms; m: f = 1). HMSN prevalence is 15.95 +/- 2.47.10(-5) being higher in rural than in urban populations. The distribution of HMSN families (total 16) in 9 districts of the region is uneven. HMSN is the most common of all hereditary muscular disorders in the region. Autosomal dominant inheritance was established in 12 families, AD gene frequency is 10.90 +/- 2.90.10(-5) gene penetrance being 90%. Sporadic cases were few (N = 4; 9.76%). No proven autosomal recessive or X-linked inheritance was found out.

[Structure and variability of hereditary disease in the Kirov Province]. / Struktura i raznoobrazie nasledstvennoi patologii v Kirovskoi oblasti.

The main purpose of this report is to present the nosological spectrum of hereditary diseases in 9 Districts of Kirov Province and to compare it with that studies earlier in other Russian populations. This comparison is undertaken in an attempt to define a "nucleus" of hereditary diseases in the Russian population studied. During this study 343 families with 546 affected were registered. The spectrum covered 55 different autosomal dominant, 14 autosomal recessive and 11 X-linked recessive hereditary disorders in the population under study. Some of these forms could be considered as common forms for the whole Russian population, because they were met in all Russian populations which were analysed. This conclusion is proved by the cluster analysis of genetic distances calculated on the basis of gene frequencies for autosomal recessive hereditary disorders.

[Further analysis of location of the gene for inborn dominant Nochurli cataract]. / Dal'neishii analiz lokalizatsii gena dominantnoi vrozhdennoi nokhurskoi katarakty.

The study of location of the gene for inborn dominant nokhur kataracta is going on. No linkage of this gene with the locus of alpha-globin gene (16p13.3) and the locus (7q36-qter) was revealed. Additional evidence was obtained for a possible location of the gene for inborn dominant nokhur kataracta on the 14 chromosome. The maximal lod value equaled to 1.089 at theta = 0.20 in the analysis of kataracta genes and alpha-1-antitrypsin (14q32.1), and 0.846 at theta = 0.30 for the kataracta gene and D14S13 (14q32.1-q32.32). For the alpha-1-antitrypsin gene the maximal lod value was 2.24 at theta = 0.05.

[Prevalence of hereditary pathologies in residents of the Kirov Province]. / Otiagoshchennost' naseleniia kirovskoi oblasti nasledstvennoi patologiei.

Medical-genetic study was carried out in the population of Kirov Province (population size about 120.000). 203 families with 334 affected with hereditary disorders were registered. The correctness of pathology classification for the inheritance type was confirmed by segregational analysis. The load of hereditary diseases in the population was: 1.25 +/- 0.06 for autosomal dominant, 1.37 +/- 0.07 for autosomal recessive and 0.22 +/- 0.06 for X-linked recessive disorders. It is suggested that variability in the values of the load of autosomal recessive disorders is determined to the large extent by genetic structure of the population.