Novel frameshift variant in the PCNT gene associated with Microcephalic Osteodysplastic Primordial Dwarfism (MOPD) Type II and small kidneys.

BACKGROUND: Microcephalic Osteodysplastic Primordial Dwarfism (MOPD) Type II is an autosomal recessive condition encompassing a heterogeneous group of disorders characterized by symmetrical growth retardation leading to dwarfism, microcephaly, and a range of multiple medical complications including neurovascular diseases. Biallelic pathogenic variants in the pericentrin gene (PCNT) have been implicated in its pathogenesis. CASE PRESENTATION: We performed whole-exome sequencing to ascertain the diagnosis of a 2 year and 6 months old boy who presented with severe failure to thrive, microcephaly, and facial gestalt suggestive of MOPD Type II which included features such as retrognathia, small ears, prominent nasal root with a large nose, microdontia, sparse scalp hair, bilateral fifth finger clinodactyly. He had a small ostium secundum atrial septal defect and bilaterally small kidneys. Microcephalic Osteodysplastic Primordial Dwarfism (MOPD) Type II was confirmed based on a pathogenic compound heterozygous frameshift variant in the PCNT gene c.5059_5060delAA | p. Asn1687fs (novel variant) and c.9535dup (p. Val3179fs). His parents were found to be heterozygous carriers for the variants. CONCLUSION: We report a novel frameshift variant in the PCNT gene and a previously unreported phenotype for Microcephalic Osteodysplastic Primordial Dwarfism (MOPD) Type II.

Mitochondrial diseases in South Asia - A systematic review.

BACKGROUND: Mitochondrial diseases are largely underdiagnosed due to their heterogeneity in clinical presentation and genotype. This is especially true for resource-constrained settings in South Asian countries such as Afghanistan, Bangladesh, Bhutan, India, Maldives, Pakistan, Nepal, Sri Lanka and Myanmar. This study aims to evaluate the current status of clinical presentations, diagnosis and treatment of Mitochondrial diseases in the South Asian region. METHODS: We undertook a systematic review of the literature on mitochondrial diseases in the South Asian region. We searched Medline, Pubmed, Cochrane library, and Google scholar using the search terms, "Mitochondrial diseases" AND "Metabolic diseases" (Mesh terms) in the title or the abstract field for each South Asian Country (Afghanistan, Bangladesh, Bhutan, India, Maldives, Pakistan, Nepal, Sri Lanka and Myanmar). RESULTS: We found 89 citations in Pubmed, 22 citations in Cochrane library and 68 in Google scholar respectively. A total of 25 non-duplicated studies met the inclusion and exclusion criteria. After assessing the quality of the published studies 18 were included. Which comprised of 17 case reports and one case-control study. CONCLUSION: Studies that were published were case reports from India, Pakistan, and Sri Lanka. Due to the paucity of published data on mitochondrial diseases in the South Asian region, it is difficult to estimate its true burden.

A Concise Review of Ketogenic Dietary Interventions in the Management of Rare Diseases.

Dietary interventions are now being used as an adjunct therapy in the treatment of rare diseases. One such method is the high-fat, moderate-protein, and very low-carbohydrate diet which produces ketosis and therefore called the ketogenic diet. Some of the more common conditions that are treated with this method are pharmacoresistant epilepsy, infantile spasms, glycogen storage diseases, and other forms of rare metabolic disturbances. With this review, we look at different uses of the ketogenic diet in treating rare diseases and the recommendations based on current evidence.

Six Novel ATM Gene Variants in Sri Lankan Patients with Ataxia Telangiectasia.

INTRODUCTION: Ataxia telangiectasia is a rare genetic condition with an estimated prevalence of 1 in 40,000-100,000 live births. This condition predominantly affects the nervous and immune systems. It is characterized by progressive ataxia beginning from early childhood. The neurological deficit associated with this condition affects one's balance, coordination, walking, and speech and can be accompanied by chorea, myoclonus, and neuropathy. They may also have ocular telangiectasias and high levels of blood alpha-fetoprotein (AFP). The ataxia telangiectasia mutated gene (ATM) is associated with this condition and codes for the ATM protein which is a phosphatidylinositol 3-kinase. This gene occupies 150 kb on chromosome 11q22-23 and contains 66 exons encoding a 13 kb transcript. ATM is a relatively large protein with a molecular weight of 350 kDa and 3,056 amino acids. METHODS: Four patients of Sri Lankan origin presenting with features suggestive of ataxia telangiectasia were referred to our genetics center for specialized genetic counseling and testing. Whole-exome sequencing followed by Sanger sequencing was used to confirm the candidate variants. Protein modeling and genotype to phenotype correlation was performed in the identified variants. RESULTS: We observed 6 novel ATM gene variants in four patients with ataxia telangiectasia. The identified variants are as follows: homozygous c.7397C > A (p.Ala2466Glu) and c.510_511delGT (p.Tyr171fs) and compound heterozygous c.5347_5350delGAAA (p.Glu1783fs), c.8137A > T (p.Arg2713 ∗ ) and c.1163A > C (p.Lys388Thr), and c.5227A > C (p.Thr1743Pro). Variant analysis was followed by modeling of the native and altered protein structures. CONCLUSION: We report novel ATM gene variants that have implications on the molecular diagnosis of ataxia telangiectasia.

Novel variant in NSDHL gene associated with CHILD syndrome and syndactyly- a case report.

BACKGROUND: Congenital hemidysplasia with ichthyosiform erythroderma and limb defects also known as CHILD syndrome is an X-linked dominant, male lethal genodermatosis with a prevalence of 1 in 100,000 live births. Mutations in NSDHL gene located at Xq28 potentially impair the function of NAD(P) H steroid dehydrogenase-like protein and is responsible for its pathogenesis. CASE PRESENTATION: The proband was a 9-month-old twin (T2) girl with a healthy twin sister (T1) of Sri Lankan origin born to non-consanguineous parents. She presented with right sided continuous icthyosiform erythroderma and ipsilateral limb defects and congenital hemidysplasia since birth. Notably the child had ipsilateral hand hypoplasia and syndactyly. There were other visceral abnormalities. We performed whole exome sequencing and found a novel heterozygous variant (NSDHL, c.713C > A, p.Thr238Asn). CONCLUSION: We report a novel missense variant in the NSDHL gene that resides in a highly-conserved region. This variant affects the NAD(P) H steroid dehydrogenase-like protein function via reduction in the number of active sites resulting in the CHILD syndrome phenotype and syndactyly.

Correction to: Three novel variants in the arylsulfatase A (ARSA) gene in patients with metachromatic leukodystrophy (MLD).

After publication of the original article [1], the authors became aware of a typographical error in the original Table 1. Nucleotide substitution c.1425C>A corresponding to amino acid change p.(Ala344Asp) should be corrected as c.1031C>A.

Variant Profile of MECP2 Gene in Sri Lankan Patients with Rett Syndrome.

Rett syndrome (RTT) is a rare monogenic disorder affecting 1 in 10,000 live female births causing severe neurodegenerative symptoms. We analyzed the molecular genetic variants in the gene encoding the methyl-CpG binding protein 2 (MECP2) of 16 girls with RTT. Their mutation profile was as follows; Already described variants: p.R168X in 25% (n = 4), p.T158M in 25% (n = 4), p.R255X in 12.5% (n = 2), p.R133C in 12.5% (n = 2), p.R294X in 6.25% (n = 1), p.K177X in 6.25% (n = 1). Novel variants: a large deletion (c.868_1188del321) in 6.25% (n = 1) and a p.X499L in 6.25% (n = 1). We also looked at the genotype to phenotype correlation of these variants. Most of the mutations were C>T in CpG hot spot as seen in other populations.

Three novel variants in the arylsulfatase A (ARSA) gene in patients with metachromatic leukodystrophy (MLD).

OBJECTIVE: To describe the genetic variants in the ARSA gene in Sri Lankan patients with metachromatic leukodystrophy (MLD). As the variant profile of MLD in the Sri Lankan population is currently unknown. RESULTS: Twenty patients from eighteen Sri Lankan families were screened for ARSA gene mutations. We found 13 different genetic variants of these three were novel. The three novel variants were p.Asp281Asn, p.Asp283Asn, p.Ala344Asp. Seven patients out of 20 were also positive for the pseudodeficiency (PD) allele c.1049A>G (p.Asn350Ser). This is the first report to describe the molecular genetic variants of Sri Lankan patients with MLD.

Two Novel Variants in the ATRX Gene Associated with Variable Phenotypes.

The X-linked alpha-thalassemia mental retardation (ATR-X) syndrome is a rare genetic condition caused by mutations in the X-encoded gene ATRX. Here we describe two unrelated patients of Sri Lankan origin with novel missense variants in the ATRX gene: c.839C>T|p.Cys280Tyr and c.5369C>T|p.Ala1790Val. These two novel variants were associated with variable phenotypes which clinically resembled X-linked mental retardation-hypotonic facies syndrome and Smith-Fineman-Myers syndrome respectively. These cases expand the clinical spectrum of ATR-X syndrome and open new opportunities for the molecular diagnosis of ATRX mutations in male patients with severe global developmental delay and intellectual disabilities.

Cenani-Lenz syndactyly syndrome - a case report of a family with isolated syndactyly.

BACKGROUND: Cenani-Lenz Syndactyly (CLS) syndrome is a rare autosomal recessive disorder characterized by syndactyly and oligodactyly of fingers and toes, disorganization and fusion of metacarpals, metatarsals and phalanges, radioulnar synostosis and mesomelic shortness of the limbs, with lower limbs usually being much less affected than upper limbs. CASE PRESENTATION: we report here two patients, born to consanguineous Sri Lankan parents, present with bilateral postaxial oligodactyly limited to upper limbs. While the proband has no noticeable facial dysmorphism, renal impairments or cognitive impairments, his affected sister displays a few mild facial dysmorphic features. Whole exome sequencing of the proband showed a novel deleterious homozygous mutation (c.1348A > G) in the LRP4 gene, resulting in an Ile450-to-Val (I450V) substitution. CONCLUSION: This recessive mutation in LRP4 confirmed the diagnosis of CLS syndrome in two patients present with isolated hand syndactyly. This is the first reported case of CLS syndrome in a family of Sri Lankan origin.

Susceptible and Prognostic Genetic Factors Associated with Diabetic Peripheral Neuropathy: A Comprehensive Literature Review.

Type 2 diabetes mellitus (T2D) is a disorder of glucose metabolism. It is a complex process involving the regulation of insulin secretion, insulin sensitivity, gluconeogenesis, and glucose uptake at the cellular level. Diabetic peripheral neuropathy (DPN) is one of the debilitating complications that is present in approximately 50% of diabetic patients. It is the primary cause of diabetes-related hospital admissions and nontraumatic foot amputations. The pathogenesis of diabetic neuropathy is a complex process that involves hyperglycemia-induced oxidative stress and altered polyol metabolism that changes the nerve microvasculature, altered growth factor support, and deregulated lipid metabolism. Recent literature has reported that there are several heterogeneous groups of susceptible genetic loci which clearly contribute to the development of DPN. Several studies have reported that some patients with prediabetes develop neuropathic complications, whereas others demonstrated little evidence of neuropathy even after long-standing diabetes. There is emerging evidence that genetic factors may contribute to the development of DPN. This paper aims to provide an up-to-date review of the susceptible and prognostic genetic factors associated with DPN. An extensive survey of the scientific literature published in PubMed using the search terms "Diabetic peripheral neuropathy/genetics" and "genome-wide association study" was carried out, and the most recent and relevant literature were included in this review.

A child with multiple congenital anomalies due to partial trisomy 7q22.1 → qter resulting from a maternally inherited balanced translocation: a case report and review of literature.

BACKGROUND: Parental balanced reciprocal translocations can result in partial aneuploidies in the offspring due to unbalanced meiotic segregation during gametogenesis. Herein, we report the phenotypic and molecular cytogenetic characterization of a 2 years and 4 months old female child with partial trisomy 7q22 → qter. This is the first such reported case resulting from a parental balanced translocation involving the long arms of chromosomes 7 and 14. The phenotype of the proband was compared with that of previously reported cases of trisomy 7q21 → qter or 7q22 → qter resulting from parental balanced translocations. CASE PRESENTATION: The proband was born pre-term to a 34-year-old mother with a history of two first trimester miscarriages and an early infant death. She was referred at the age of 8 months for genetic evaluation due to prenatal and postnatal growth retardation, developmental delay and multiple congenital anomalies. On clinical evaluation, she had craniofacial dysmorphic features such as scaphocephaly, large anterior fontanelle with open posterior fontanelle, prominent occiput, triangular face, high forehead, hypertelorism, down slanting eyes, flat nasal bridge, small nose, low set ears, micro-retrognathia, high arched palate and short neck. Cranial computerized tomography scan showed lateral ventriculomegaly with features of early cerebral atrophy. Conventional cytogenetic analysis showed the karyotype 46,XX,der(14)t(7;14)(q22;q32)mat in the proband due to an unbalanced segregation of a maternal balanced translocation t(7;14)(q22;q32). Fluorescence in-situ hybridization analysis confirmed the partial trisomy 7q22 → qter in the proband with a minimal loss of genetic material on chromosome 14. Single nucleotide polymorphism array further confirmed the duplication on chromosome 7q22.1 → qter and a small terminal deletion on chromosome 14q32.3 → qter. CONCLUSION: We report the longest-surviving child with trisomy 7q22 → qter due to a parental balanced translocation between chromosomes 7 and 14. Clinical features observed in the proband were consistent with the consensus phenotype of partial trisomy 7q22 → qter reported in the scientific literature. Early diagnosis of these patients using molecular cytogenetic techniques is important for establishing the precise diagnosis and for making decisions pertaining to the prognostication and management of affected individuals.

Population Screening for Hemoglobinopathies.

Hemoglobinopathies are the most common single-gene disorders in the world. Their prevalence is predicted to increase in the future, and low-income hemoglobinopathy-endemic regions need to manage most of the world's affected persons. International organizations, governments, and other stakeholders have initiated national or regional prevention programs in both endemic and nonendemic countries by performing population screening for α- and ß-thalassemia, HbE disease, and sickle cell disease in neonates, adolescents, reproductive-age adults (preconceptionally or in the early antenatal period), and family members of diagnosed cases. The main aim of screening is to reduce the number of affected births and, in the case of sickle cell disease, reduce childhood morbidity and mortality. Screening strategies vary depending on the population group, but a few common screening test methods are universally used. We discuss the salient features of population-screening programs around the globe as well as current and proposed screening test methodologies.

Spectrum of low-density lipoprotein receptor (LDLR) mutations in a cohort of Sri Lankan patients with familial hypercholesterolemia - a preliminary report.

BACKGROUND: Hypercholesterolemia is a major determinant of cardiovascular disease-associated morbidity and mortality. Mutations in the LDL-receptor (LDLR) gene are implicated in the majority of the cases with familial hypercholesterolemia (FH). However, the spectrum of mutations in the LDLR gene in Sri Lankan patients has not been investigated. The objective of this study was to report the frequency and spectrum of variants in LDLR in a cohort of Sri Lankan patients with FH. METHODS: A series of consecutive patients with FH, diagnosed according to Modified Simon Broome criteria or Dutch Lipid Clinic Network criteria at the University Medical Unit, Colombo, were recruited. Clinical data was recorded. DNA was extracted from peripheral blood samples. The LDLR gene was screened for genetic variants by Sanger sequencing. RESULTS: A total of 27 patients [13 (48%) males, 14 (52%) females; age range 24-73 years] were tested. Clinical features found among these 27 patients were: xanthelasma in 5 (18.5%), corneal arcus in 1 (3.7%), coronary artery disease (CAD) in 10 (37%), and a family history of hypercholesterolemia and/or CAD in 24 (88.9%) patients. In the entire cohort, mean total cholesterol was 356.8 mg/dl (±66.4) and mean LDL-cholesterol was 250.3 mg/dl (±67.7). Sanger sequencing of the 27 patients resulted in the identification of known pathogenic missense mutations in 5 (18.5%) patients. Four were heterozygotes for 1 mutation each. They were c.682G > C in 2 patients, c.1720C > A in 1 patient, and c.1855 T > A in 1 patient. One patient with severe FH phenotypes was a compound heterozygote for one known mutation, c.2289G > T, and another missense variant, c.1670C > G (p.Thr557Ser), with unknown functional impact. This latter variant has not been reported in any other population previously. CONCLUSIONS: The frequency of known mutations in the LDLR gene in this cohort of patients was markedly low compared to frequencies reported in other populations. This highlights the likelihood of a complex, polygenic inheritance of FH in Sri Lankan patients, indicating the need for a comprehensive genetic evaluation that includes the screening for mutations in other genes that cause FH, such as APOB, PCSK9, and LDLRAP1.

Partial trisomy 16q21➔qter due to an unbalanced segregation of a maternally inherited balanced translocation 46,XX,t(15;16)(p13;q21): a case report and review of literature.

BACKGROUND: Partial trisomy is often the result of an unbalanced segregation of a parental balanced translocation. Partial trisomy16q is characterized by a common, yet non-specific group of craniofacial dysmorphic features, and systemic malformations with limited post-natal survival. Most of the cases of partial trisomy 16q described in the scientific literature have reported only one, or less frequently two cardiac defects in the affected babies. Herein, we report a case of partial trisomy 16q21➔qter with multiple and complex cardiac defects that have not previously been reported in association with this condition. CASE PRESENTATION: We report the phenotypic and cytogenetic features of a Sri Lankan female infant with partial trisomy 16q21➔qter. The baby had a triangular face with downslanting eyes, low set ears and a cleft palate. Systemic abnormalities included multiple cardiac defects, namely double outlet right ventricle, ostium secundum atrial septal defect, mild pulmonary stenosis, small patent ductus arteriosus, and bilateral superior vena cavae. An anteriorly placed anus was also observed. The proband was trisomic for 16q21➔qter chromosomal region with a karyotype, 46,XX,der(15)t(15;16)(p13;q21)mat. The chromosomal anomaly was the result of an unbalanced segregation of a maternal balanced translocation; 46,XX,t(15;16)(p13;q21). Partial trisomy 16q was established by fluorescence in-situ hybridization analysis. CONCLUSIONS: The craniofacial dysmorphic features and the presence of cardiac and anorectal malformation in the proband are consistent with the phenotypic spectrum of partial trisomy 16q reported in the scientific literature. More proximal breakpoints in chromosome 16q are known to be associated with multiple cardiac abnormalities and poor long-term survival of affected cases. This report presents a unique case with multiple, complex cardiac defects that have not previously been described in association with a distal breakpoint in 16q. These findings have important diagnostic and prognostic implications.

Phenotypic and Cytogenetic Characterization of Mesenchymal Stromal Cells in De Novo Myelodysplastic Syndromes.

Bone marrow (BM) mesenchymal stem/stromal cells (MSCs) are vital in hematopoiesis. Whether BM-MSCs alter their characteristics in Myelodysplastic Syndromes (MDS) is still controversial. We characterized MSCs of de novo MDS patients in Sri Lanka who have not been reported previously in the literature. We also analyzed MSCs derived from different MDS subtypes. MSCs were culture-expanded, characterized by flow cytometry, and induced towards osteogenic and adipogenic differentiation. Growth properties were determined using growth curves and population doubling times. Karyotyping and FISH were performed on MSCs. Cell morphology, differentiation potential, and CD marker expression of MDS-MSCs of all subtypes were comparable to those of control-MSCs. No significant growth differences were observed between control MSCs and MDS-MSCs of all subtypes (p > 0.05). 31% of MDS-MSCs had chromosomal aberrations (der(3),del(6q),del(7p), loss of chromosomes) whose BM karyotypes were normal. Highest percentage of karyotypic abnormalities was observed in RCMD-MSCs. Patients with abnormal BM karyotypes had no aberrant MSC clones. Results show that in spite of presence of genetically abnormal clones in MDS-MSC populations, in vitro phenotypic and growth characteristics of MSCs in MDS remain unchanged. Further, the occurrence of genetic abnormalities in BM-MSCs in MDS could be considered as an autonomous event from that of their hematopoietic counterparts.

Ring Chromosome 4 in a Child with Multiple Congenital Abnormalities: A Case Report and Review of the Literature.

A female child born preterm with intrauterine growth retardation and presenting with facial dysmorphism with clefts, microcephaly, limb deformities, and congenital abnormalities involving cardiovascular and urinary systems is described. Chromosomal analysis showed a de novo 46,XX,r(4)(p15.3q35) karyotype. The clinical features of the patient were compared with the phenotypic characteristics of 17 previously reported cases with ring chromosome 4 and those with Wolf-Hirschhorn syndrome (4p-). Clinical features observed in this case are consistent with the consensus phenotype in ring chromosome 4. Patent ductus arteriosus and bilateral talipes equinovarus observed in this baby widen the phenotypic spectrum associated with ring chromosome 4.

Optimizing amniotic membrane tissue banking protocols for ophthalmic use.

Amniotic membrane (AM) due to its anti-inflammatory, anti-scarring and anti-angiogenic properties is used as corneal and wound grafts. When developing AM tissue banks, cell viability, membrane morphology and genomic stability should be preserved following cryopreservation. To analyze the changes rendered to the AM during the process of cryopreservation by comparing different combinations of standard cryopreservation media; fetal bovine serum (FBS), dimethyl sulfoxide (DMSO), Dulbecco's modified eagle's medium (DMEM) and glycerol at -80 °C and at -196 °C for a period of 6 weeks and at 4 °C in 70 % alcohol for 6 weeks. Following informed consent, placentae of healthy term pregnancies delivered by elective Cesarean section were collected and AM separated into 5 × 5 cm size sections and under sterile conditions stored in 9:1 DMSO:FBS and 1:1 DMEM:Glycerol at -196 and -80 °C for 6 weeks. Similar sections were also stored at 4 °C in 70 % alcohol for 6 weeks. After storage periods following were assessed; AM epithelial cell viability by trypan blue vital stain, epithelial cell proliferation capacity by cell doubling time, membrane morphology by haematoxylin and eosin (H&E) stain and genomic stability by conventional G-banded karyotyping. Human amniotic epithelial cells were cultured in DMEM and 10 % FBS in humidified atmosphere of 5 % carbon dioxide at 37 °C and were characterized using RT-PCR for Octamer-binding protein 4 (Oct-4) and glucose-6-phosphate dehydrogenase (G6PD) genes. All the above parameters were also assessed in fresh AM. AM obtained from 4 term placentae. Mean cell count and mean cell doubling times in days respectively; for fresh AM 3.8 × 10(6); 1.59, after 6 weeks in DMSO:FBS at -196 °C 3.0 × 10(6); 2.38 and at -80 °C 2.1 × 10(6); 1.60, in DMEM:Glycerol at -196 °C 3.6 × 10(6); 2.33 at -80 °C 23 × 10(6); 1.66 and at 4 °C 3.3 × 10(6); 2.14. Histology analysis of the fresh AM showed an intact epithelial monolayer, thick basement membrane (BM) and avascular stromal matrix. Amniotic membranes stored at -196 °C showed morphology similar to fresh AM in both preservation media and AM stored at -80 °C showed disruption of the stromal matrix. At 4 °C the epithelial monolayer showed flattening. Fresh AM karyotype was 46XX. Analyzable spreads for karyotype were not obtained from stored AMs. Human amniotic epithelial cells were positive for both Oct-4 and G6PD genes. AM is best preserved at -196 °C either in 1:9 DMSO:FBS or 1:1 DMEM:Glycerol. In both conditions cell viability and membrane integrity were shown to be preserved up to 6 weeks. Since analyzable chromosome spreads from cell cultures were not obtained, genomic stability could not be assessed.

A study of HLA-B∗15:02 in a Sri Lankan population: Implications for pharmacogenomic testing.

HLA-B∗15:02 is known as a biomarker for carbamazepine (CBZ) induced Steven-Johnson Syndrome and Toxic Epidermal Necrolysis (SJS/TEN) in some Asian populations. Hence United States Federal Drug Administration (USFDA) recommends HLA-B∗15:02 screening for Asian and other populations with a high prevalence of HLA-B∗15:02, prior to the administration of carbamazepine. This study was conducted to estimate the prevalence of HLA-B∗15:02 in a cohort of Sri Lankans. We observed an overall prevalence of 4.3% (4/93) among 93 Sri Lankans comprising 32 Sinhalese, 30 Sri Lankan Tamils and 31 Moors. The allele was detected in 3 [9.3%; 3/32] Sinhalese, 0 [0%; 0/30] Sri Lankan Tamils and in 1 [3%; 1/31] Moor. The overall prevalence of HLA-B∗15:02 in this population was close to that of other populations where the USFDA has recommended HLA-B∗15:02 screening. A larger study is required to confirm these findings, especially among the Sinhalese where the frequency appears to be high.