Whole genome sequencing identifies a homozygous nonsense mutation in the JPH2 gene in Shih Tzu dogs with progressive retinal atrophy.

Progressive retinal atrophy (PRA), common autosomal recessive disorder affecting several dog breeds including Shih Tzu, is characterized by degeneration of photoreceptors leading to blindness. To identify PRA genetic variants, three affected and 15 unaffected Shih Tzu and 20 non-Shih Tzu were recruited. Dogs underwent ophthalmologic examination and electroretinography, revealing hallmark retina pathological changes and an abnormal electroretinography in all affected dogs but not in unaffected dogs. WGS was performed. Non-synonymous homozygous variants were searched in coding regions of genes involved in retinal diseases/development; the criterion was that variants should only be present in affected dogs and should be absent in both unaffected and 46 genomes of dogs (from an available evolutionary database). Only one out of the 109 identified variants is predicted to harbor a high-impact consequence, a nonsense c.452A>C (p.L151X) in the JPH2 gene. The genotype of JPH2 variant in all 38 dogs was determined with Sanger sequencing. All three affected dogs, but none of the 35 unaffected, were homozygous for the nonsense variant. JPH2 has been previously found to be expressed in several excitable cells/tissues including retina photoreceptors. Hence, JPH2 is a candidate gene for PRA in Shih Tzu.

Dental properties, ultrastructure, and pulp cells associated with a novel DSPP mutation.

OBJECTIVE: To investigate physical characteristics and behaviours of dental pulp cells of teeth isolated from a dentinogenesis imperfecta (DGI) patient with a novel dentin sialophosphoprotein (DSPP) mutation. SUBJECTS AND METHODS: Whole exome and Sanger sequencing were employed to identify mutations. Physical characteristics of the teeth were examined. Pulp cells' behaviours including cell proliferation, colony-forming unit, osteogenic differentiation, pluripotent markers, and mesenchymal stem cell markers were investigated. RESULTS: The proband had opalescent brown primary teeth with extensive loss of enamel. Mutation analysis revealed a novel heterozygous 4-bp deletion, c.1915_1918delAAGT (p.K639QfsX674), in exon 5 of the DSPP associated with DGI. Analysis of the extracted primary incisor demonstrated a decrease in brightness but an increase in yellow and red chroma. The dentin showed reduced mineral density. The dentinal tubules were present in the predentin, but progressively collapsed in the dentin. The pulp cells exhibited markedly reduced CD105 expression, decreased cell proliferation, and smaller colony-forming units. CONCLUSIONS: We identified a novel mutation in the DSPP gene which disturbed dentin characteristics and pulp cells' behaviours. Our study expands the mutation spectrum and understanding of pathologic dentin phenotypes related to the frameshift deletion in the dentin phosphoprotein (DPP) region of the DSPP gene.

A novel PITX2 mutation in non-syndromic orodental anomalies.

OBJECTIVE: To identify orodental characteristics and genetic aetiology of a family affected with non-syndromic orodental anomalies. SUBJECTS AND METHODS: Physical and oral features were characterised. DNA was collected from an affected Thai family. Whole-exome sequencing was employed to identify the pathogenic variants associated with inherited orodental anomalies. The presence of the identified mutation was confirmed by Sanger sequencing. RESULTS: We observed unique orodental manifestations including oligodontia, retained primary teeth, taurodont molars, peg-shaped maxillary central incisors, high attached frenum with nodule and midline diastema in the proband and her mother. Mutation analyses revealed a novel heterozygous frameshift deletion, c.573_574delCA, p.L193QfsX5, in exon 5 of PITX2A in affected family members. The amino acid alterations, localised in the transcriptional activation domain 2 in the C-terminus of PITX2, were evolutionarily conserved. Mutations in PITX2 have been associated with autosomal-dominant Axenfeld-Rieger syndrome and non-syndromic eye abnormalities, but never been found to cause isolated oral anomalies. CONCLUSIONS: This study for the first time demonstrates that the PITX2 mutation could lead to non-syndromic orodental anomalies in humans. We propose that the specific location in the C-terminal domain of PITX2 is exclusively necessary for tooth development.

Severe Hyperammonemic Encephalopathy Requiring Dialysis Aggravated by Prolonged Fasting and Intermittent High Fat Load in a Ramadan Fasting Month in a Patient with CPTII Homozygous Mutation.

BACKGROUND: Carnitine palmitoyltransferase II (CPTII) deficiency is a mitochondrial fatty acid oxidation disorder that can present antenatally as congenital brain malformations, or postnatally with lethal neonatal, severe infantile, or the most common adult myopathic forms. No case of severe hyperammonemia without liver dysfunction has been reported. CASE PRESENTATION: We described a 23-year-old man who presented to the emergency department with seizures and was found to have markedly elevation of serum ammonia. Continuous renal replacement therapy was initiated with successfully decreased ammonia to a safety level. He had a prolonged history of epilepsies and encephalopathic attacks that was associated with high ammonia level. Molecular diagnosis revealed a homozygous mutation in CPTII. The plasma acylcarnitine profile was consistent with the diagnosis. Failure to produce acetyl-CoA, the precursor of urea cycle from fatty acid in prolonged fasting state in Ramadan month, worsening mitochondrial functions from circulating long chain fatty acid and valproate toxicities were believed to contribute to this critical metabolic decompensation. CONCLUSION: Fatty acid oxidation disorders should be considered in the differential diagnosis of hyperammonemia even without liver dysfunction. To our knowledge, this is the first case of CPTII deficiency presented with severe hyperammonemic encephalopathy required dialysis after prolonged religious related fasting.

A novel GJA1 mutation in oculodentodigital dysplasia with extensive loss of enamel.

OBJECTIVE: To characterize clinical features and identify genetic causes of a patient with oculodentodigital dysplasia (ODDD). SUBJECTS AND METHODS: Clinical, dental, radiological features were obtained. DNA was collected from an affected Thai family. Whole-exome sequencing was employed to identify the disease-causing mutation causing ODDD. The presence of the identified variant was confirmed by Sanger sequencing. RESULTS: The proband suffered with extensive enamel hypoplasia, polysyndactyly and clinodactyly of the 3rd-5th fingers, microphthalmia, and unique facial characteristics of ODDD. Mutation analysis revealed a novel missense mutation, c. 31C>A, p.L11I, in the GJA1 gene which encodes gap junction channel protein connexin 43. Bioinformatics and structural modeling suggested the mutation to be pathogenic. The parents did not harbor the mutation. CONCLUSIONS: This study identified a novel de novo mutation in the GJA1 gene associated with severe tooth defects. These results expand the mutation spectrum and understanding of pathologic dental phenotypes related to ODDD.

Novel mutations in the FUCA1 gene that cause fucosidosis.

Fucosidosis is a rare lysosomal storage disorder inherited in an autosomal recessive manner. Its estimated frequency is below 1 in 200,000 live births. Its clinical phenotypes include progressive neurological and mental deterioration, coarse facial features, growth retardation, visceromegaly, angiokeratomas, and seizures. The disease is caused by mutations in the FUCA1 gene that lead to deficiency of a-L-fucosidase. Here, we describe the clinical and molecular features of a Thai boy with fucosidosis. Whole exome sequencing and array-based comparative genomic hybridization analysis revealed that the patient was compound heterozygous for a single base-pair deletion (c.670delC; p.P224LfsX2) inherited from his father, and a 3281-base-pair deletion covering exon 3 inherited from his mother. Neither mutation has been reported before so the FUCA1 mutational spectrum is herein expanded.

Whole-exome sequencing reveals a novel COL2A1 mutation in a patient with spondylo-epiphyseal dysplasia congenita.

Skeletal dysplasia is a group of disorders with more than 450 entities, many of which cannot be differentiated, especially during infancy, but could lead to different clinical courses and prognoses. In this study, we have described a case of a Thai infant with short stature, flat face, pectus carinatum, indirect inguinal hernia, platyspondyly, and generalized delayed endochondral ossification. Using whole-exome sequencing (WES), we successfully identified a de novo heterozygous mutation, c.2024G>A (p.G675D), in the COL2A1 gene, which, to our knowledge, has not been previously reported. These molecular findings helped provide a definite diagnosis of spondyloepiphyseal dysplasia congenita, aiding in proper management of the disease and improved genetic counseling. We demonstrated that WES is an efficient and cost-effective tool for molecular diagnosis for a type II collagenopathy.

Pyridoxal 5ꞌ-phosphate-responsive epilepsy with novel mutations in the PNPO gene: a case report.

Pyridoxal 5'-phosphate (PLP)-responsive epilepsy is a rare autosomal recessive epileptic disorder caused by deficiency of pyridox(am)-ne 5'-phosphate oxidase (PNPO). Neonatal onset seizures in PLP responsive epilepsy are usually resistant to common anticonvulsants and pyridoxine, but respond to PLP. Various PNPO mutations are associated with this disorder. In this report, we have described a case of a female baby with neonatal onset seizures responding to PLP. Exome sequencing revealed that the patient was compound heterozygous for pathogenic mutations [c.546+1G>A (IVS5+1 G>A) and c.620delG (p.G207VfsX215)] in the PNPO gene. The c.546+1G>A was inherited from the mother while the c.620delG was inherited from the father. Both mutations were absent in 122 unrelated Thai controls. The results of this study indicated the presence of two newly identified mutations in this Thai patient with PLP-responsive epilepsy for the first time, expanding the mutational spectrum of PNPO.

Clinical and molecular characterization of Thai patients with Wiskott-Aldrich syndrome.

Wiskott-Aldrich syndrome (WAS) is an X-linked recessive primary immunodeficiency disorder caused by mutations in the gene encoding the WAS protein (WASP). Classic WAS is characterized by thrombocytopenia with small-sized platelets, recurrent infections, eczema and increased susceptibility to autoimmune diseases and haematologic malignancies. Here, we reported on seven unrelated Thai individuals with classic WAS. In addition to clinical and immunologic characterization, mutation analysis by PCR-sequencing the entire coding region of WASP was performed. Recurrent and novel mutations were successfully identified. A nonsense mutation, the c.55C>T (p.Q19X), has not been previously described, expanding the mutational spectrum of WASP. The patient with this newly described mutation developed cow's milk allergy manifesting as angioedema and urticaria and had cytomegalovirus infection that was successfully treated with long-term ganciclovir. This study reported long-term follow-up of seven patients with molecular confirmation of WAS and infrequent features in the patient with classic WAS carrying the novel nonsense mutation.

Association of CD247 with systemic lupus erythematosus in Asian populations.

OBJECTIVE: Systemic lupus erythematosus (SLE) is a prototypic autoimmune disease with complex genetic inheritance. CD247 (CD3Z, TCRZ) plays a vital role in antigen recognition and signal transduction in antigen-specific immune responses, and is known to be involved in SLE pathogenesis. Weak disease association was reported for genetic variants in this gene in Caucasian studies for SLE, Crohn's disease and systemic sclerosis, but its role as a genetic risk factor was never firmly established. METHODS: In this study, using a collection of 612 SLE patients and 2193 controls of Chinese ethnicity living in Hong Kong in a genome-wide study, single nucleotide polymorphisms (SNPs) in and around CD247 were identified as being associated with SLE. The two most significant SNPs in this locus were selected for further replication using TaqMan genotyping assay in 3339 Asian patients from Hong Kong, Mainland China, and Thailand, as well as 4737 ethnically and geographically matched controls. RESULTS: The association of CD247 with SLE in Asian populations was confirmed (rs704853: odds ratio [OR] = 0. 81, p = 2.47 × 10(-7); rs858543: OR = 1.10, p = 0.0048). Patient-only analysis suggested that rs704853 is also linked to oral ulcers, hematologic disorders and anti-double-stranded DNA (dsDNA) antibody production. CONCLUSION: A significant association between variants in CD247 and SLE was demonstrated in Asian populations. Understanding the involvement of CD247 in SLE may shed new light on disease mechanisms and development of new treatment paradigms.

Pathogenic mechanism of mutations in the thyroid hormone receptor ß gene.

BACKGROUND: Resistance to thyroid hormone (RTH) is characterized by a variable degree of reduced tissue sensitivity to thyroid hormone (TH). It is usually caused by mutations in the TH receptor-ß (TRß) gene. AIMS: To characterize clinical and molecular features of a Thai patient with RTH. Functional significance of the identified mutation as well as other uncharacterized TRß mutations was also investigated. MATERIALS AND METHODS: Exons 3-10 of the TRß gene were assessed by PCR-sequencing. Functional characterization of the mutant TRß was determined by the luciferase reporter system. RESULTS: A mutation in exon 9 of the TRß gene resulting in a methionine to threonine substitution at codon 313 was identified. The functional consequence of this mutation and other uncharacterized known mutations (p.I276L, p.I280S, p.L330S, p.G344A, p.M442T) was evaluated by transfection studies. Four out of 6 had a significant impairment of T3-dependent transactivation. When co-transfected with the wild-type TRß, all exhibited a dominant negative effect. CONCLUSION: A de novo mutation was identified in the patient with clinical diagnosis of RTH. Our findings provide a strong support that interfering with the T3-mediated transcriptional activation of the wild-type TRß independent of the ability to activate transcription is a major pathogenic mechanism causing RTH.

Holocarboxylase synthetase deficiency: novel clinical and molecular findings.

Multiple carboxylase deficiency (MCD) is an autosomal recessive metabolic disorder caused by defective activity of biotinidase or holocarboxylase synthetase (HLCS) in the biotin cycle. Clinical symptoms include skin lesions and severe metabolic acidosis. Here, we reported four unrelated Thai patients with MCD, diagnosed by urine organic acid analysis. Unlike Caucasians, which biotinidase deficiency has been found to be more common, all of our four Thai patients were affected by HLCS deficiency. Instead of the generally recommended high dose of biotin, our patients were given biotin at 1.2 mg/day. This low-dose biotin significantly improved their clinical symptoms and stabilized the metabolic state on long-term follow-up. Mutation analysis by polymerase chain reaction-sequencing of the entire coding region of the HLCS gene revealed the c.1522C>T (p.R508W) mutation in six of the eight mutant alleles. This suggests it as the most common mutation in the Thai population, which paves the way for a rapid and unsophisticated diagnostic method for the ethnic Thai. Haplotype analysis revealed that the c.1522C>T was on three different haplotypes suggesting that it was recurrent, not caused by a founder effect. In addition, a novel mutation, c.1513G>C (p.G505R), was identified, expanding the mutational spectrum of this gene.

Prenatal diagnosis of a novel mutation, c.529C>T (p.Q177X), in the BCKDHA gene in a family with maple syrup urine disease.

Maple syrup urine disease (MSUD) is an autosomal recessive metabolic disorder caused by defective activity of the branched-chain alpha-keto-acid dehydrogenase (BCKD) complex. The disease-causing mutations can affect the BCKDHA, BCKDHB or DBT genes encoding for the E1a, E1b, and E2 subunits, respectively, of the BCKD complex. Here we report a girl who first presented to our clinic at 4 years of age with profound mental retardation. A diagnosis of MSUD was subsequently made based on the results of plasma amino acid analysis. Mutation analysis confirmed that she was homozygous for a novel mutation, c.529C>T (p.Q177X) in BCKDHA, while both parents, who were first cousins, were heterozygous. This enabled us to give an option of prenatal diagnosis to the parents. The prenatal testing for MSUD was performed during the mother's subsequent pregnancy and revealed that the fetus was heterozygous for the mutation. The healthy male neonate was born and his genotype was tested by restriction enzyme analysis, which confirmed the result of the prenatal testing. In summary, a late diagnosis of MSUD in patients without an unusual odour could occur especially in countries without neonatal screening programs as seen in the index patient. Mutation detection was, however, still beneficial to the family since prenatal testing could be performed in subsequent pregnancies. In addition, a novel mutation was found, expanding the mutation spectrum of this disease.

Bilateral submandibular gland aplasia with clinico-radiological mass due to prolapsing sublingual salivary tissue through mylohyoid boutonniere: a case report and review.

Aplasia of major salivary glands is very rare. Compensatory hypertrophy of the rest of the glands can result in clinico-radiological masses. We present a report of a rare case of non-syndromic bilateral submandibular gland aplasia with hypertrophied sublingual salivary tissue, the latter herniating through mylohyoid boutonnière to present as a palpable mass on the left side with corresponding CT findings. Multiplanar evaluation is emphasised by utilizing multidetector CT.

Study of the poliovirus receptor related-1 gene in Thai patients with non-syndromic cleft lip with or without cleft palate.

Non-syndromic cleft lip with or without cleft palate (CL/P) has a complex etiology with several genetic and environmental factors playing a role. The poliovirus receptor related-1 gene (PVRL1) has been shown to underlie a syndromic form of CL/P and, in some populations, contribute to non-syndromic CL/P. To investigate whether mutations in PVRL1 play a part in the formation of non-syndromic CL/P in the Thai population, 100CL/P patients were analyzed for mutations in PVRL1 by polymerase chain reaction amplification and direct sequencing of all the coding regions of its alpha isoform. Of this series of patients, one was found to be heterozygous for 1183G>A in exon 6, expected to result in the substitution of a valine by a methionine at position 395 (V395M). This mutation was not found in 200 unaffected Thai control individuals. The valine position is conserved across all known mammalian PVRL1 sequences. In conclusion, a novel non-synonymous PVRL1 mutation was found in a Thai patient with non-syndromic CL/P, suggesting a possible etiologic role of PVRL1 in non-syndromic CL/P across different populations.

Three novel mutations in the PORCN gene underlying focal dermal hypoplasia.

Focal dermal hypoplasia (FDH) is an X-linked dominant disorder characterized by patchy dermal hypoplasia with digital, ocular and dental abnormalities. Very recently, mutations in the PORCN gene were demonstrated to cause FDH. Here, we described three unrelated Thai girls who were sporadic cases of FDH. One of them had unilateral athelia, which has never been described in FDH. Mutation analysis by polymerase chain reaction sequencing the entire coding regions of PORCN successfully revealed three potentially pathogenic mutations, c.373+1G>A, c.737_738insA and c.1094G>A (p.R365Q). One was found in each of three patients. In addition, another sequence variant c.682C>T (p.R228C) with an inconclusive role was found in one patient and her unaffected mother. The two missense mutations were not detected in at least 100 ethnic-matched control chromosomes, and all four mutations had never been previously described. X chromosome inactivation studies showed random patterns in all of them. This study demonstrates that PORCN is the gene responsible for FDH across different populations and extends the total number of confirmed mutations to 26.

TBX22 mutations are a frequent cause of non-syndromic cleft palate in the Thai population.

Mutations in the TBX22 gene underlie an X-linked malformation syndrome with cleft palate (CP) and ankyloglossia. Its mutations also result in non-syndromic CP in some populations. To investigate whether mutations in TBX22 play a part in the formation of non-syndromic CP in the Thai population, we performed mutation analysis covering all the coding regions of the TBX22 gene in 53 unrelated Thai patients with non-syndromic CP. We identified four potentially pathogenic mutations, 359G-->A (R120Q), 452G-->T (R151L), 1166C-->A (P389Q), and 1252delG in four different patients. All mutations were not detected in at least 112 unaffected ethnic-matched control chromosomes and had never been previously reported. R120Q and R151L, found in two sporadic cases, were located in the DNA binding T-box domain. P389Q and 1252delG, found in two familial cases, were at the carboxy-terminal region, which has never been described. Our study indicates that TBX22 mutations are responsible for a significant proportion of Thai non-syndromic CP cases confirming its importance as a frequent cause of non-syndromic CP across different populations.