University of Colombo e-Repository

UCER (University of Colombo Electronic Repository) is a collection of scientific research publications by researchers at the University of Colombo, Sri Lanka. This e-Repository serves to manage, preserve and make available the academic works of the faculty, postgraduate students, and research groups. The collection includes faculty publications, master's and doctoral theses abstracts. This repository is updated regularly, and new works are added to collections on a continuous basis

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Authors are responsible for obtaining copyright permission from the publisher and submitting the signed declaration to ir@lib.cmb.ac.lk.

Recent Submissions

Implementation of a cloud-based bioinformatics pipeline for genetic variant discovery of next generation sequence data linked to hereditary cancer syndromes
(University of Colombo, 2020) Neththikumara, N.F.; Wetthasinghe, T.K.; Dissanayake, V.H.W.
Introduction: Next generation sequencing (NGS) has now become the norm for medical diagnostics worldwide. Sequencing data used for genetic variant discovery consists of millions of short sequences called reads. Depending on the platform used for sequencing, the reads have different properties like pairing, length and error-rate which can significantly impact the analysis and variant calling process. Thus, analysing NGS data using bioinformatics techniques has become a challenge in terms of complexity, efficiency and cost effectiveness. Methods: Index cases and at-risk family members of patients with hereditary cancer syndromes have been recruited for studies conducted in the Human Genetics Unit. These individuals have been sequenced by the Illumina Miseq NGS sequencer, with the Trusight Cancer library enrichment kit. An automated bioinformatics pipeline has been developed to analyse these data, which process mapping, filtering, realignment, recalibration, variant calling and annotation. Each module has been integrated together using python and bash scripts. A secondary variant analysis module was also implemented to systematically prioritize variants in genes associated with hereditary cancer syndromes. The pipeline has been deployed to a dedicated cloud server utilizing the Google cloud computing engine and cloud storage services. Results: This pipeline generates a fully annotated variant calling file (VCF) of single nucleotide polymorphisms (SNPs) and short insertions and deletions (Indels) with several data quality statistics reports. It also incorporates virtual gene panels to generate a variant list in a subset of genes associated with a specific hereditary cancer syndrome, with in-silico pathogenicity predictions for each variant. The amount of sample data that can be run at a given time is presumed to be unlimited, as the pipeline is fully scalable. Conclusion: The incorporation of custom bioinformatics pipelines into the sequencing workflow enables reliable, efficient and cost-effective data analysis for disease diagnosis.
Buerger’s angle and Pole test for chronic limb threatening ischaemia patients with diabetes
(University of Colombo, 2020) Godakandage, M. H. P.; Abeysekara, W. P. A. M.; Basnayake, B. M. O. D.; Gunawardena, R. M. T. M.; Abeywickrama, S. S.; Saseekaran. B.; Paviththiran, S.; Boulton, J. A.; Cassim, M. R. N.; Wijeyaratne, S. M.
Introduction: Quantification of chronic limb threatening ischaemia (CLTI) is widely done using ankle brachial pressure index (ABPI), toe pressure (TP) or transcutaneous oximetry (TcPO2). In diabetes, ankle level pressures are unreliable due to medial calcification of vessels. Ulcers and gangrene limit using TP and TcPO2. We explored the Buerger’s angle and the pole test; combined with continuous wave Doppler to identify CLTI. Methods: Consecutive 40 limbs in 28 diabetes patients assessed. ABPI was assessed following standard protocol. With the Doppler probe placed over ankle level anterior tibial and posterior tibial arteries sequentially, legs were slowly elevated until the signal was lost. The leg elevation angle (with femur greater trochanter as the pivot point) and the heights were documented, and the highest values analysed. Results: Majority were males [67.8% (19)]. Mean age was 64.14(39-83). Five (17.9%) had chronic kidney disease. Thirteen limbs (32.5%) were asymptomatic; 8(20%) had rest pain and 24(60%) had tissue loss. ABPI (0.38 – more than 1) was categorized as <0.4, 0.4-0.59, 0.6-0.79, 0.8 and more. The angle (12- 90 degrees) was categorized as < 30, 30-60 and 60-90. Height ranged 21-90cm. Linear regression reveal significant difference between ABPI, and Buerger’s angle (r= 0.467, p= 0.002) and the height (r = 0.440, p = 0.004). Angle categories are also significantly different(p=0.034). Conclusions: Leg elevation angle and pole test does not correlate with ABPI in this sample. These tests may be more accurate, and easier to perform than ABPI. However larger samples and follow up are necessary for its validation and implementation.
Identifying PROZ G79A gene variant in a cohort of patients
(University of Colombo, 2020) Chamara, N.D.P.; Noordeen, N.; Wetthasinghe, T.K.; Dissanayake, V.H.W.
Introduction: Ischemic stroke in younger adults is far less common than among older adults. The underlying risk factors are more diverse. Approximately 10%-15% of all strokes occur in adults ages 18-50. The diagnosis of stroke in younger adults can be challenging to differentiate from stroke mimics and to identify the cause or underlying pathogenesis. There are more than 50 monogenic diseases that can cause stroke. Given the increasing incidence of early-onset stroke, there is an objective need for early detection. The aim of this study was to identify genetic variants associated in a cohort of Sri Lankan patients affected with young stroke in Sri Lanka. Methods: A literature review was conducted to determine the genetic variants associated with young stroke. A novel tetra-primer amplification refractory mutation system-polymerase chain reaction (T-ARMS-PCR) was performed to determine the presence of PROZ G79A gene variant/s known to be prevalent in the Asian region. The optimized assay was Sanger validated. The genotyping was done using 90 samples from patients who had given prior consent for such studies. Results: Out of the ninety patients 57 were homozygous for the normal variant, 22 were heterozygotes for the pathogenic variant while 11 patients were homozygous for the pathogenic variant. The minor allele frequency for the g.79G>A genotype was 0.244 (chi squared = 11.79) according to the Hardy Weinberg equilibrium. Conclusion: PROZ G79A variant is a genetic marker for symptomatic young stroke. This genotypic assay can be implemented as a sensitive, specific and simple diagnostic technique for screening associated genetic variants for young stoke.
Dr. Google - assessing quality of information and readability of internet searches available to the patient
(University of Colombo, 2020) Saleem, F.S.; Xavier, C.S.; Wickramasinghe, D.P.; Samarasekera, D.N.
Introduction: With the dawn of the internet era, assessing information seems to be within the reach of our fingertips, as seen by the increasing google search trends. There is, however, no assurance on the quality, validity and readability of the available information This study aims to assess the quality of information and the degree of readability on the internet regarding inguinal hernia in adults. Methods: We used ‘Google’ as our primary search engine and ran a search for the term ‘INGUINAL HERNIA’. The analysis was confined to the first 20 searches aimed at adult patients. Each website was then analysed with the JAMA benchmark, DISCERN tool, the presence or absence of the health on the internet seal (HON). The pages were also scored using the Flesch Kincaid Grade Level (FKGL) Flesch Reading Ease (FRE) score, and automated readability index (ARI). Results: The average JAMA score was 2.84 with seven of the twenty webpages reaching a maximum of four points (35%). The majority scored two or below. The average DISCERN score was 53.2% with only one website achieving a maximum of 80 (5%). A fifth of the pages scored less than 50% of the total. The HON seal was present only in four of the twenty webpages (20%). The median FRE value for the pages was 43.9 (IQR 42.8-58.4). Four (21%) of the 19 pages read above the minimum readability standard of 60. The FKGL score gave a median of 11.25 (IQR 9.05-12.0) with seven pages (36.8%) reaching a standard of eight. The median for ARI was 16.8 (IQR 15.2-16.8) with 16 pages that read above standard. A Spearman bivariate analysis of FKGL against FRE showed a significant negative correlation (-0.933, p=0.01)) and a bivariate analysis of FKGL against ARI showed a positive correlation (0.342, p=0.01). All the pages were in English and free. Conclusions: Although there are many websites related to inguinal hernia, a large proportion were poorly written with shortcomings. These need to be addressed to ensure the patients’ accessibility to reliable, easy to read information on the internet.
Umbilical hernia in adults: According to Google, M.D.
(University of Colombo, 2020) Xavier, C.S.; Murugiah, T.; Saleem, F.S.; Wickramasinghe, D.P.; Samarasekera, D.N.
Background: Patients are increasingly using the internet for health-related information, especially umbilical hernias, according to Google search trends. We aimed to evaluate the quality and readability of information available on the internet regarding umbilical hernia in adults. Methods: We searched on Google, Yahoo and Bing using the keywords “umbilical hernia” AND “adults”. Results from the first two pages were included. We excluded webpages with restricted access, non-text media, and exclusive paediatric content. After removing duplicates, 27 unique webpages were evaluated independently by two co-authors using 3 standard criteria: the DISCERN tool, JAMA benchmarks, and the HON seal. 26 of the webpages (1 page was encrypted) were also scored using FRE, FKGL, and ARI readability scores. The results were then combined and analysed. Results: Inter-rater agreement for DISCERN scores between the two co-authors was good (Weighted Kappa = 0.63 ± 4.6%, CI=95%). Both co-authors agreed on JAMA benchmarks and the HON seal. The average DISCERN score was 43 (53.8%). The average JAMA score was 2.2, with eight (30%) of the 27 unique webpages scoring the maximum of 4 points. The HON seal was present on 8 webpages (30%). The median FRE, FKGL, and ARI scores were 50.0 (IQR= 44.4 – 58.4), 10.2 (IQR = 9.2 - 11.4), and 9.3 (IQR = 8.0 – 10.6) respectively. Six (23%) of the 26 pages met the minimum FRE standard of 60 and ARI standard of 8, while only five (19%) of the webpages met the FKGL standard of 8. There was a strong positive correlation between FKGL and ARI (Spearman rho = 0.947, p < 0.001). Conclusion: Though there are some webpages that provide good quality and easily readable information regarding umbilical hernias, the overall quality and readability is far from ideal.