WNT10B mutations associated with isolated dental anomalies.

Isolated hypodontia is the most common human malformation. It is caused by heterozygous variants in various genes, with heterozygous WNT10A variants being the most common cause. WNT10A and WNT10B are paralogs that likely evolved from a common ancestral gene after its duplication. Recently, an association of WNT10B variants with oligodontia (severe tooth agenesis) has been reported. We performed mutational analysis in our cohort of 256 unrelated Thai families with various kinds of isolated dental anomalies. In 7 families afflicted with dental anomalies we detected 4 heterozygous missense variants in WNT10B. We performed whole exome sequencing in the patients who had WNT10B mutations and found no mutations in other known hypodontia-associated genes, including WNT10A, MSX1, PAX9, EDA, AXIN2, EDAR, EDARADD, LPR6, TFAP2B, LPR6, NEMO, KRT17, and GREM2. Our findings indicate that the variants c.475G>C [p.(Ala159Pro)], found in 4 families, and c.1052G>A [p.(Arg351His)], found in 1 family, are most probably causative. They also show that WNT10B variants are associated not only with oligodontia and isolated tooth agenesis, but also with microdontia, short tooth roots, dental pulp stones, and taurodontism.

DETECTING PORCN MICRODELETIONS IN A LARGE FAMILY WITH FOCAL DERMAL HYPOPLASIA.

Focal dermal hypoplasia (FDH), an X-linked dominant disease with a highly variable phenotype, presents mainly with congenital linear pigmentation of the skin, herniation of fat through the dermal defects and multiple papillomas. PORCNmicrodeletions are identified in a total of 12 FDH patients to date. Routine molecular methods for detecting microdeletions have proven not to be effective, as patients also carry a normal allele. Additionally, methods using copy number estimations are labor-intensive, time-consuming and require expensive equipment. With respect to the molecular diagnosis of FDH, we aimed to investigate the inheritance of maternal disease allele in a three-generation FDH pedigree with seven affected members by using a simple yet efficient method. The strategy used in this study appeared to have the benefit of detecting all PORCN micro-deletions identified for FDH so far. The family with the largest number of related patients reported to date presented an opportunity to evaluate clinical variability, which was high, with the least affected and the most severely affected patients being half-sisters. The extensive intra-familial phenotypic variability observed in this FDH family suggests that genetic counselling should be part of management of this syndrome even in a family with a very mild case. The unique finding of IgA deficiency in the most severe case indicated that the feature could be a new characteristic of FDH.

Carrier detection by DNA analysis in Duchenne muscular dystrophy families.

We applied DNA analysis techniques to Turkish families whose members were afflicted with Duchenne/Becker muscular dystrophy. The aim of this study was to establish a prenatal diagnosis of this anomaly and to determine the carrier state. All of the techniques used in established diagnosis centers are now applied routinely in our laboratory. Both Southern analysis and polymerase chain reaction (PCR) methods were used for deletion detection in patients and restriction enzyme fragment length polymorphism (RFLP) determination for linkage analysis in women at risk. CA repeated sequence length polymorphism, the most recent technique for linkage analysis, was also applied. About 250 individuals from seventy-nine families were investigated and thirty-six entire families were screened. Twenty-five women were found to be carriers while thirty seven were non-carriers. The carrier state could not be determined in three women.

Termination sites for adenovirus type 2 DNA replication.

Termination sites for replication of adenovirus type 2 DNA have been demonstrated at both ends of the viral chromosome by the procedure of Danna and Nathans (1972). Single-stranded DNA from replicating intermediates was also characterized by hybridization with separated strands of viral DNA. The results indicate that both strands are exposed during replication.

Dinucleotide repeat polymorphism at 11q23.

A highly polymorphic CA repeat sequence was identified near the NCAM gene on chromosome 11q23. It should be a useful marker in the localization of genes responsible for neurological disorders that are known to map to this region.

Separation of the minimal replication region of the F plasmid into a replication origin segment and a trans-acting segment.

An analysis was carried out on the replication functions within a 2.3 kilobase (kb) segment of the F plasmid which contains an origin (ori s) of replication and is capable of autonomous replication in Escherichia coli. Two separable regions were delineated for this segment: an origin region of approximately 1,140 bp in length and a segment of approximately 1,140 bp that functions in trans to support replication of the origin region. The trans-acting segment is functional as part of an F replicon or when inserted into the E. coli chromosome. A prominent feature of the trans-acting segment is a coding sequence for a 29 K protein (Murotsu et al. 1981).

Direct repeats of the F plasmid incC region express F incompatibility.

The nucleotide sequence of the incompatibility region incC, located at 45.8--46.4 kb on the F plasmid map, was determined. This region consists of 543 bp and contains sufficient information to code for only two small polypeptides of 34 and 30 amino acids each. Deletion of the ATG start codons for these two polypeptides has no effect on expression of incC incompatibility. A prominent feature of this sequence is the presence of five 22 bp direct repeats. A 58 bp segment of the incC region that contains two of these direct repeats was inserted into plasmid pACYC184, which is compatible with the F plasmid. The pACYC184 plasmid containing the direct-repeat sequences now expresses incompatibility with the F'lac plasmid and replication-proficient derivatives of the mini-F plasmid.

Sequence of inverted terminal repetitions from different adenoviruses: demonstration of conserved sequences and homology between SA7 termini and SV40 DNA.

We have established the nucleotide sequence for the inverted terminal repetition of human adenovirus type 3, a subgroup B adenovirus. The repetition, which is 136 bp long, shows a high degree of homology with the known sequence for the inverted repetition of adenovirus type 5 (Steenbergh et al., 1977) a subgroup C adenovirus. Partial sequence information convering 120 bp of the inverted terminal repetitions of human serotype 12, a subgroup A member, and of simian adenovirus type 7 has also been obtained. A comparison of the established sequences shows that the terminal repetitions, in particular the first 50 bp from the ends, contain sequences that have been well conserved in adenovirus evolution. For instance, only six mismatched base pairs were detected among the first 50 bp in the repetitions of simian adenovirus type 7 and human adenovirus type 5, although the homology between simian adenovirus 7 and human subgroup C adenoviruses was estimated to be only 30%. A 14 bp sequence located 9-22 nucleotides from the ends is present in DNAs from all the human serotypes examined as well as in simian adenovirus 7 DNA. Furthermore, the simian adenovirus 7 repetition contains a 21 bp sequence which is present in SV40 DNA, close to the origin of DNA replication.

Repair of radiation-induced strand breaks as related to the inducible inhibitor of postirradiation DNA degradation.

The repair of radiation-produced single-strand breaks observed under alkaline conditions is very apparent in cells which possess an inducible inhibitor of postirradiation DNA degradation. Previous induction of the inhibitor with ultraviolet light increases the amount of repair. In those cells which are genetically not inducible there is no increase following ultraviolet irradiation.

Frequency of the 35delG mutation in the connexin 26 gene in Turkish hearing-impaired patients.

The 35delG mutation in the connexin 26 gene (GJB2) at the DFNB1 locus is the most common mutation in patients with autosomal-recessive sensorineural deafness. Genetic diagnosis is crucial for genetic counseling. We have developed an easy and simple method and screened a total of 235 unrelated hearing-impaired children. We found 48 of the subjects to be homozygous for the mutation, including 27 of 83 familial cases, 15 of 101 singletons, 4 of 9 subjects born to assortative marriages (deaf married to deaf), and 2 of 42 subjects for whom the parents claimed an environmental factor as the etiology of the condition. The high ratio of individuals homozygous for the mutation indicated that the 35delG mutation in the connexin gene accounts for more than 90% of the mutations at this locus.

Nature of the single-stranded DNA in replicating adenovirus type 5 DNA.

Single-stranded regions in replicating adenovirus type 5 DNA were isolated and hybridized in solution to the separated strands of adenovirus 2 or 5 DNA. The results showed that the two strands of adenovirus 5 DNA are exposed to almost the same extent during replication, suggesting that displacement synthesis may start from either end of the viral DNA.

Two complementary strand-specific termination sites for adenovirus DNA replication.

Adenovirus type 2 DNA, specifically labeled at the termini for DNA replication, was prepared by isolation of viral DNA molecules which were completed during short pulses with 3H-thymidine. The distribution of radioactivity in the two complementary strands at the termini for DNA replication was determined by liquid phase hybridization and gelelectrophoresis. At the right-hand terminus, nearly all radioactivity was found in the viral h strand, whereas at the left-hand terminus, most radioactivity was confined to the viral l strand. The results suggest that both molecular ends serve as origins and termini for replication of adenovirus type 2 DNA.

Purification of RNA-DNA hybrids by exclusion chromatography.

A simple method for selection of RNA-DNA hybrids has been developed and applied to the purification of adenovirus-specific messenger RNA. Cytoplasmic RNA prepared from adenovirus type 2 (ad2)-infected HeLa cells or from an ad2-transformed rat cell line was hybridized in solution to the complementary strands of ad2 DNA. The hybridization mixture was subsequently fractionated by chromatography on a Sepharose 2B column. The intact probe DNA as well as the RNA-DNA hybrids are excluded from the gel matrix and elute with the void volume. Nonhybridized RNA, in contrast, is included into the gel matrix and elutes as a broad peak well separated from the excluded fractions. Fractions corresponding to the void volume, were collected and the RNA-DNA hybrids were denatured in 90% formamide. The selected RNA was separated from the DNA by affinity chromatography on poly(U)-Sepharose. Restriction endonuclease fragments of DNA with a large enough size to make them excluded from the agarose column were also used for hybridization. In these experiments hybridizations were carried out under conditions which would allow R-loop formation (Thomas, M., White, R.L., and Davis, R.W. (1976) Proc. Natl. Acad. Sci. U.S.A. 73, 2294-2298) and the hybridized RNA was separated from unhybridized RNA by Sepharose chromatography. The validity of the method was demonstrated by programming an in vitro protein-synthesizing system with selected RNA.

From Asia to Europe: mitochondrial DNA sequence variability in Bulgarians and Turks.

Two hypervariable sequence segments in the control region of mitochondrial DNA were determined in samples of Bulgarians and Turks. The Turkish sample presented a higher degree of internal diversity, in terms of total number of variable nucleotides, as well as in the average pairwise nucleotide difference. Pairwise difference distributions were built for both samples, yielding smooth bell shapes in agreement with the Rogers and Harpending model. The Bulgarian and Turkish data were compared with several European and W. Asian Caucasoid populations (Basques, Tuscans, Sardinians, British, Middle Easterners and Indians). Mean pairwise differences suggest that a demographic expansion occurred sequentially in the Middle East, through Turkey, to the rest of Europe (Bulgaria included). Current mutation rate estimates date this expansion in times ranging between 50,000 and 100,000 years ago and, thus, would correspond to the arrival of anatomically modern humans in Europe. Sequence trees for segment I show that European and Middle Eastern sequences derived from the reference sequence. Coalescence times for segment I sequences agree with those predicted by pairwise distributions. Genetic trees were constructed between populations and revealed an extreme homogeneity between European samples.

The novel genetic disorder microhydranencephaly maps to chromosome 16p13.3-12.1.

We studied a large consanguineous Anatolian family with children who exhibited hydranencephaly associated with microcephaly. The children were severely affected. This novel genetic disorder is autosomal recessive. We used autozygosity mapping to identify a locus at chromosome 16p13.3-12.1; it has a LOD score of 4.11. The gene locus is within a maximal 11-cM interval between markers D16S497 and D16S672 and within a minimal critical region of 8 cM between markers D16S748 and D16S490.

Analysis of fragile X-mental retardation families using flanking polymorphic DNA probes.

Fragile-X mental retardation (FRAX-MR) is one of the more common X-linked disorders affecting 1 in 1,500 newborn males. This disease is characterized by the expression of fragile site in the region q27.3 of the X-chromosome of affected boys when their lymphocytes are cultured in folate deficient medium. In most patients there is macroorchidism postpubertally. The clinical diagnosis of carrier females based on the expression of fragile site in Xq27.3 is usually difficult and sometimes impossible. About half of the carrier females escape diagnosis by this method. Furthermore, prenatal diagnosis is not always feasible. Using Restriction Fragment Length Polymorphism (RFLP) and cloned DNA segments from the region Xq27-Xqter as probes, we have investigated Swedish families with FRAX-MR in three generations. Interesting observations, previously unreported to our knowledge, have been made in some patients and carrier mothers, using one of the probes which is localized to the distal end of Xq. The significance of these findings and the linkage of the disease locus to the different probes used in this study is presented.

DNA analysis in Turkish Duchenne/Becker muscular dystrophy families.

The molecular genetics of Duchenne/Becker muscular dystrophy was investigated in 81 affected Turkish families. Deletions were detected by multiplex polymerase chain reaction assays and cDNA Southern analyses. The distribution of the deletions along the gene and their correlation to clinical phenotype were different from the studies reported on other populations. Moreover, DNA polymorphisms in mothers were determined using 8 DNA probes and three CA repeat sequences, and a high degree of informativeness was observed.

Deletion pattern in the dystrophin gene in Turks and a comparison with Europeans and Indians.

Patterns of dystrophin gene deletions in DMD/BMD patients were compared in four populations: Turks (n = 146 deletions), Europeans (n = 838), North Indians (n = 89), and Indians from all over India (n = 103). Statistical tests revealed that there are differences in the proportions of small deletions. In contrast, the distribution of deletion breakpoints and the frequencies of specific deletions commonly observed in the four populations are not significantly different. The variations strongly suggest that sequence differences exist in the introns, and the differences are in agreement with genetic distances among populations. The similarities suggest that some intronic sequences have been conserved and that those will trigger recurrent deletions, since it is unlikely that gene flow would disperse the deleted chromosomes, which vanish from the gene pool in a few generations.

A high frequency of distinct ATM gene mutations in ataxia-telangiectasia.

The clinical features of the autosomal recessive disorder ataxia-telangiectasia (AT) include a progressive cerebellar ataxia, hypersensitivity to ionizing radiation, and an increased susceptibility to malignancies. Epidemiological studies have suggested that AT heterozygotes may also be at increased risk for malignancy, possibly as a consequence of radiation exposure. A gene mutated in AT patients (ATM) has recently been isolated, making mutation screening in both patients and the general population possible. Because of the relatively large size of the ATM gene, the design of screening programs will depend on the types and distribution of mutations in the general population. In this report, we describe 30 mutations identified in a panel of unrelated AT patients and controls. Twenty-five of the 30 were distinct, and most patients were compound heterozygotes. The most frequently detected mutation was found in three different families and had previously been reported in five others. This corresponds to a frequency of 8% of all reported ATM mutations. Twenty-two of the alterations observed would be predicted to lead to protein truncation at sites scattered throughout the molecule. Two fibroblast cell lines, which displayed normal responses to ionizing radiation, also proved to be heterozygous for truncation mutations of ATM. These observations suggest that the carrier frequency of ATM mutations may be sufficiently high to make population screening practical. However, such screening may need to be done prospectively, that is, by searching for new mutations rather than by screening for just those already identified in AT families.