Medicine
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This repository contains the published and unpublished research of the Faculty of Medicine by the staff members of the faculty
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Item Development of a low cost semiquantitative polymerase chain reaction assay for molecular diagnosis of williams syndrome(Clinical Laboratory Publications, 2024) Ranaweera, D.M.; de Silva, D.C.; Samarasinghe, D.; Perera, S.; Kugalingam, N.; Samarasinghe, S.R.; Madushani, W.Y.; Jayaweera, H.H.E.; Gunewardene, S.; Muneeswaran, K.; Gnanam, V.S.; Chandrasekharan, N.V.BACKGROUND: Williams Beuren Syndrome (WBS) is a well-recognized and common genetic cause of congenital heart defects, developmental delay, hypercalcemia, and characteristic facial features. It is caused by a 1.5 - 1.8 Mb heterozygous deletion of chromosome 7q11.23 with loss of around 28 coding genes. The aim of this study was to develop a low-cost, semi-quantitative PCR (sqPCR) method to detect the chromosome 7q11.23 deletion. METHODS: Twenty-four suspected WBS cases were recruited following ethical clearance and informed consent. Blood was obtained, DNA extracted and spectrophotometrically quantified using standard methods. To detect the deletion by dosage analysis, a target region within a gene located in the WBS commonly deleted region of 7q11.23 was amplified together with a control region in a duplex sqPCR assay. The control region was telomeric to the WBS commonly deleted region and was located in chromosome 7q31.2. The two target regions within the deleted region namely a locus within ELN and a marker in the intergenic region between FZD9 and FKBP6 and designated IFF, were amplified in separate duplex sqPCR assays. The Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene was used as the control for normalization. Included in the assay were a non-deleted and deleted individuals' samples. RESULTS: Nineteen patients were identified to have the deletion while five did not. All 24 patients' results were confirmed by whole exome sequencing and 11 also by fluorescence in-situ hybridization (FISH). CONCLUSIONS: The data obtained indicates the sqPCR assay developed in this study to be an accurate and reliable diagnostic test for WBS. Most Sri Lankan patients with WBS are diagnosed clinically, as many parents of affected WBS children are unable to afford currently available molecular diagnostic testing. This low cost sqPCR test is therefore likely to benefit Sri Lankan WBS patients, by enabling genetic testing for confirming or refuting a clinical diagnosis of WBS and may be of use in other low and middle income countries.Item Genome sequencing in families with congenital limb malformations(Springer-Verlag., 2021) Elsner, J.; Mensah, M.A.; Holtgrewe, M.; Hertzberg, J.; Bigoni, S.; Busche, A.; Coutelier, M.; de Silva, D.C.; Elçioglu, N.; Filges, I.; Gerkes, E.; Girisha, K.M.; Graul-Neumann, L.; Jamsheer, A.; Krawitz, P.; Kurth, I.; Markus, S.; Megarbane, A.; Reis, A.; Reuter, M.S.; Svoboda, D.; Teller, C.; Tuysuz, B.; Türkmen, S.; Wilson, M.; Woitschach, R.; Vater, I.; Caliebe, A.; Hülsemann, W.; Horn, D.; Mundlos, S.; Spielmann, M.ABSTRACT: The extensive clinical and genetic heterogeneity of congenital limb malformation calls for comprehensive genome-wide analysis of genetic variation. Genome sequencing (GS) has the potential to identify all genetic variants. Here we aim to determine the diagnostic potential of GS as a comprehensive one-test-for-all strategy in a cohort of undiagnosed patients with congenital limb malformations. We collected 69 cases (64 trios, 1 duo, 5 singletons) with congenital limb malformations with no molecular diagnosis after standard clinical genetic testing and performed genome sequencing. We also developed a framework to identify potential noncoding pathogenic variants. We identified likely pathogenic/disease-associated variants in 12 cases (17.4%) including four in known disease genes, and one repeat expansion in HOXD13. In three unrelated cases with ectrodactyly, we identified likely pathogenic variants in UBA2, establishing it as a novel disease gene. In addition, we found two complex structural variants (3%). We also identified likely causative variants in three novel high confidence candidate genes. We were not able to identify any noncoding variants. GS is a powerful strategy to identify all types of genomic variants associated with congenital limb malformation, including repeat expansions and complex structural variants missed by standard diagnostic approaches. In this cohort, no causative noncoding SNVs could be identified.Item Biallelic variants in DNA2 cause microcephalic primordial dwarfism.(Wiley-Liss, 2019) Tarnauskaitė, Z.; Bicknell, L.S.; Marsh, J.A.; Murray, J.E.; Parry, D.A.; Logan, C.V.; Bober, M.B.; de Silva, D.C.; Duker, A.L.; Sillence, D.; Wise, C.; Jackson, A.P.; Murina, O.; Reijns, M.A.M.Microcephalic primordial dwarfism (MPD) is a group of rare single-gene disorders characterised by extreme reduction in brain and body size from early development onwards. Proteins encoded by MPD-associated genes play important roles in fundamental cellular processes, notably genome replication and repair. Here we report identification of four MPD individuals with biallelic variants in DNA2, which encodes an ATP-dependent helicase/nuclease involved in DNA replication and repair. We demonstrate that the two intronic variants (c.1764-38_1764-37ins(53) and c.74+4A>C) found in these individuals substantially impair DNA2 transcript splicing. Additionally we identify a missense variant (c.1963A>G), affecting a residue of the ATP-dependent helicase domain that is highly conserved between humans and yeast, with the resulting substitution (p.Thr655Ala) predicted to directly impact ATP/ADP binding by DNA2. Our findings support pathogenicity of these variants as biallelic hypomorphic mutations, establishing DNA2 as an MPD-disease gene. This article is protected by copyright. All rights reserved.Item Peer evaluation of individual effort in student group work(Sri Lanka Medical Association, 2007) Roshini, A.A.N.; de Silva, D.C.; Chandratilake, M.N.; Pathmeswaran, A.OBJECTIVE: To assess the feasibility of using a method of peer assessment of individualized effort during group work and to validate it. DESIGN, SETTING AND METHODS: At the end of a module during the 2nd year, 12 groups of medical students (consisting of 13-14 students per group) made a presentation. Foilowing the presentation, the students assessed the contribution of each of their colleagues towards the presentation by using a rating form. This form listed the members of the group and consisted of a global assessment of each student's contribution to group work as well as assessment of contribution in eight different ways. An individualized mark was calculated for each student by summarizing the scores assigned to him/ her by other group members. Each student was given their personal mark and was asked for their reaction. RESULTS: Peer assessment marks were available for all 164 students. Nineteen (11.6%) students had got less than 50 marks. Though 11 of these students were not satisfied with their mark, 12 (63%) accepted that the mark reflected their contribution. Among those who had scored 50 or more marks, 87% were satisfied with their marks and 88% stated that the marks reflected their contribution to group work. CONCLUSION: The second year medical students taking part in this study were prepared to assess their peers and most of them were satisfied with the marks allocated by their peers. Over 60% of those who scored less than 50 marks accepted that their mark was a fair reflection of their contribution to group work.Item Congenital generalized lipodystrophy: identification of novel variants and expansion of clinical spectrum.(John Wiley & Sons, 2016) Haghighi, A.; Kavehmanesh, Z.; Haghighi, A.; Salehzadeh, F.; Santos-Simarro, F.; Van Maldergem, L.; Cimbalistiene, L.; Collins, F.; Chopra, M.; Al-Sinani, S.; Dastmalchian, S.; de Silva, D.C.; Bakhti, H.; Garg, A.; Hilbert, P.Congenital generalized lipodystrophy (CGL) is an autosomal recessive disorder with two major subtypes. Variants in AGPAT2 result in CGL type 1 with milder manifestations, whereas BSCL2 variants cause CGL type 2 with more severe features. Muscle hypertrophy caused by lack of adipose tissue is present early in life in CGL patients. Our aim was to investigate 10 CGL patients from 7 different countries and report genotype-phenotype relationships. Genetic analysis identified disease-causing variants in AGPAT2 (five patients) and in BSCL2 (five patients), including three novel variants; c.134C>A (p.Ser45*), c.216C>G (p.Tyr72*) in AGPAT2 and c.458C>A (p.Ser153*) in BSCL2. We also report possible novel clinical features such as anemia, breast enlargement, steatorrhea, intraventricular hemorrhage and nephrolithiasis in CGL patients. Generalized lipodystrophy and muscular hypertrophy were the only features in all of our patients. Hepatomegaly was the second common feature. Some manifestations were exclusively noticed in our CGL2 patients; hypertrichosis, high-pitched voice and umbilical hernia. Bone cysts and history of seizures were noticed only in CGL1 patients. The findings of this study expand our knowledge of genotype-phenotype correlations in CGL patients. These results have important clinical applications in diagnosis and management of the CGL patients as well as in genetic counseling in families at-risk. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.Item Evaluation of 22q11.2 deletion in Cleft Palate patients.(Mumbai : Medknow Publications, 2012) Prabodha, L.B.; Dias, D.K.; Nanayakkara, B.G.; de Silva, D.C.; Chandrasekharan, N.V.; Ileyperuma, I.BACKGROUND: Cleft palate is the commonest multifactorial epigenetic disorder with a prevalence of 0.43-2.45 per 1000. The objectives of this study were to evaluate the clinical features and identify the 22q11.2 deletion in patients with cleft palate in Sri Lanka. MATERIALS AND METHODS: Cleft patients attending a Teaching Hospital in Sri Lanka were recruited for this study. The relevant data were obtained from review of case notes, interviews, and examination of patients according to a standard evaluation sheet. Quantitative multiplex polymerase chain reaction (PCR) was performed to identify the 22q11.2 deletion. A gel documentation system (Bio-Doc) was used to quantify the PCR product following electrophoresis on 0.8% agarose gel. RESULTS AND CONCLUSION: There were 162 cleft palate patients of whom 59% were females. A total of 92 cleft palate subjects (56.2%) had other associated clinical features. Dysmorphic features (25.27%) and developmental delays (25.27%) were the commonest medical problems encountered. The cleft was limited to the soft palate in 125 patients, while in 25 patients it involved both the hard and the soft palate. There were seven subjects with bifid uvula and five subjects with submucous cleft palate. None of the patients had 22q11.2 deletion in this study population. A multicentered large population-based study is needed to confirm the results of this study and to develop guidelines on the appropriate use of 22q11.2deletion testing, which are valid for cleft palate patients in Sri Lanka.Item FGFR1 mutations cause Hartsfield syndrome, the unique association of holoprosencephaly and ectrodactyly(British Medical Association, 2013) Simonis, N.; Migeotte, I.; Lambert, N.; Perazzolo, C.; de Silva, D.C.; Dimitrov, B.; Heinrichs, C.; Janssens, S.; Kerr, B.; Mortier, G.; Van Vliet, G.; Lepage, P.; Casimir, G.; Abramowicz, M.; Smits, G.; Vilain, C.BACKGROUND: Harstfield syndrome is the rare and unique association of holoprosencephaly (HPE) and ectrodactyly, with or without cleft lip and palate, and variable additional features. All the reported cases occurred sporadically. Although several causal genes of HPE andectrodactyly have been identified, the genetic cause of Hartsfield syndrome remains unknown. We hypothesised that a single key developmental gene may underlie the co-occurrence of HPE and ectrodactyly. METHODS: We used whole exome sequencing in four isolated cases including one case-parents trio, and direct Sanger sequencing of three additional cases, to investigate the causative variants in Hartsfield syndrome. RESULTS: We identified a novel FGFR1 mutation in six out of seven patients. Affected residues are highly conserved and are located in the extracellular binding domain of the receptor (two homozygous mutations) or the intracellular tyrosine kinase domain (four heterozygous de novo variants). Strikingly, among the six novel mutations, three are located in close proximity to the ATP's phosphates or the coordinating magnesium, with one position required for kinase activity, and three are adjacent to known mutations involved in Kallmann syndrome plus other developmental anomalies. CONCLUSIONS: Dominant or recessive FGFR1 mutations are responsible for Hartsfield syndrome, consistent with the known roles of FGFR1 in vertebrate ontogeny and conditional Fgfr1-deficient mice. Our study shows that, in humans, lack of accurate FGFR1 activation can disrupt both brain and hand/foot midline development, and that FGFR1 loss-of-function mutations are responsible for a wider spectrum of clinical anomalies than previously thought, ranging in severity from seemingly isolated hypogonadotropic hypogonadism, through Kallmannsyndrome with or without additional features, to Hartsfield syndrome at its most severe end.Item Soto syndrome: a rare overgrowth disorder(Sri Lanka Medical Association, 2013) de Silva, D.C.; de Leeuw, N.; Gunasekera, R.This is a case report of a boy with an overgrowth syndrome called Soto syndrome (cerebral gigantism).Item Attitudes toward prenatal diagnosis and termination of pregnancy for genetic disorders among healthcare workers in a selected setting in Sri Lanka(Wiley, 2008) de Silva, D.C.; Jayawardana, P.; Hapangama, A.; Suraweera, E.G.D.N.; Ranjani, D.; Fernando, S.; Karunasena, C.; Jinadasa, S.Item Adrenal hypersecretion(Sri Lanka Medical Association, 2007) Wijesiriwardena, B.; de Silva, D.C.Hypersecretion from the adrenal glands is associated with hypertension. Causes include Conn syndrome, Cushing syndrome and phaechromocytoma. This article discusses their clinical features, diagnosis and treatment as well as the management of incidentally identified adrenal tumours (incidentaloma).