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Moatter T, Ahmed S, Majid H, Jafri L, Bilal M, Najumuddin, Faisal, Khan AH. Sequence variants in the BTD underlying biotinidase deficiency in families of Pakistani origin. J Gene Med 2024; 26:e3597. [PMID: 37751899 DOI: 10.1002/jgm.3597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/02/2023] [Accepted: 09/03/2023] [Indexed: 09/28/2023] [Imported: 10/18/2023] Open
Abstract
BACKGROUND Biotinidase deficiency (BTD) is a rare autosomal recessive metabolic disease, which develops neurological symptoms because of the impaired biotin recycling. Pathogenic mutations on BTD gene cause BTD deficiency. The clinical features and mutation analysis of Pakistani children with BTD deficiency have rarely been described. Herein, for the first time, we report the clinical features, BTD gene mutations and biochemical analysis of seven symptomatic children with BTD deficiency from Pakistan. METHODS Seven suspected BTD-deficient patients who presented abnormal organic acid profiles and clinical features were subjected to Sanger sequencing to identify pathogenic mutations in the BTD gene. The results were analyzed by Mutation Surveyor Software. RESULTS All seven patients exhibited common biotinidase deficiency symptoms including hypotonia, developmental delay and seizures. Biochemical analysis shows marked excretion of 3-hydroxy isovalerate in all cases, followed by 3-hydroxy propionate and methyl citrate. Sanger sequencing revealed one frame-shift mutation, c.98_104delinsTCC (p.Cys33Phefs), and two missense mutations, c.1612C>A (p.Arg538Ser) and c.1330G>C (p.Asp444His). All mutations were in the homozygous state and classified as pathogenic in published studies and mutation databases. CONCLUSIONS This study has validated the BTD variants as the underlying cause of biotinidase deficiency in which molecular testing of BTD is supported by urinary organic acid analysis and clinical diagnosis. Secondly, the strength of the local availability of this test in Pakistan will paved the way for the neonatal screening of biotinidase deficiency.
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Ahmed S, Agravatt AK, Siddiqui A, Jafri L, Siddiqui I. Indirect Reference Intervals of Serum Calcium in Pakistani Children Using KOSMIC, Bhattacharya, and Hoffman Approach. Clin Lab 2023; 69. [PMID: 37702687 DOI: 10.7754/clin.lab.2023.230305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023] [Imported: 10/18/2023]
Abstract
BACKGROUND Reference intervals (RIs) of serum calcium vary based on age, population demographics, and methods of assessment. However, conventional approaches to establish serum calcium (Ca)RIs pose ethical and practical challenges, especially in the pediatric population. Hence, the use of indirect approaches is beneficial. This study was carried out to estimate the RIs of serum Ca using three indirect approaches in the pediatric and adolescent population of Pakistan. METHODS Data mining laboratory information systems, for serum Ca results from 2013 - 2021 was done on a target population ranging from birth to 18 years of age. The population was grouped into three categories based on age (birth - 1 year, 2 - 4 years, and 5 - 18 years), as defined previously by Tahmasebi et al. in the CALIPER cohort. Pre-validated indirect algorithms, 'KOSMIC', Bhattacharya, and Hoffman, were used for analyzing the RIs. RESULTS A total of non-duplicate 40,914 serum Ca tests were retrieved over a period of 6 years, including 38.7% (n = 15,830) from birth - 1 year, 16.3% (n = 6,641) from > 1 - 4 years, and 45.2% (n = 18443) from > 4 - 18 years respectively. The three methods revealed comparable performance with the direct RIs reported by Tahmasebi et al. in the CALIPER cohort. Keeping a stringent total allowable error of 1 mg/dl for Serum Ca as given by Clinical Laboratory Improvement Amendments (CLIA) the KOSMIC method outperformed the other two when compared to Tahmasebi, Houman, et al. Conclusions: The study advocates the use of the indirect approach for calculating RIs for serum calcium in the pediatric population, especially to aid clinical decision making in a low resource setting, due to its ability to reproduce results in line with the direct approach in a more economical, practical, and feasible way.
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Majid H, Jafri L, Farooqui AJ, Ahmed S, Nisa Khan ZU, Khan AH. Factors Associated With Awareness Of Literate Mothers About Newborn Screening: A Cross-Sectional Study From A Low-Middle-Income Country. J PAK MED ASSOC 2023; 73:1805-1810. [PMID: 37817688 DOI: 10.47391/jpma.7004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/12/2023] [Imported: 10/18/2023]
Abstract
Objectives To explore the awarenesslevel of literate mothersregarding newborn screening programmes, and to evaluate the associated factors. METHODS The descriptive, cross-sectional study was conducted at the Section of Chemical Pathology, Department of Pathology andLaboratoryMedicine,AgaKhanUniversity,Karachi,fromJanuary toSeptember 2021, andcomprisedmothers aged 18 years or more. Data was collected using a structured questionnaire about newborn screening, and the subjects were compared in terms of age, residential background, education and parity. Data was analysed using SPSS 23. RESULTS Of the 1016 responses, 896(88.2%) were analysed. The mean age of the sample was 37.7±10.87 years. There were 470(52.4%) mothers aged 31-45 years, 859(95.87%) were from urban areas, 751(84%) had a graduate degree, 652(72.7%) weremultiparous andhad824(91.9%)hadhealthy children.Overall, 386 (43%)mothershadawarenessofnewbornscreening programmes. The main factors associated with awareness were age, education, primiparity, having healthy children, and province ofresidencebeing Sindh andPunjab(p<0.05),while the urban-ruraldividedwas not a significantfactor(p=0.737). Cost of healthcare 417(46.5%) and lack of awareness among physicians 356(39.7%) were identified asthe main challenges in establishing newborn screening servicesin the country. CONCLUSIONS The awareness among mothers about new born screening programmes was generally low among the subjects studied.
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Ahmed S, Akbar F, DeBerardinis RJ, Ni M, Afroze B. Evaluation of the clinical, biochemical, and genetic presentation of neonatal and adult-onset 5,10-methylene tetrahydrofolate reductase (MTHFR) deficiency in patients from Pakistan. J Pediatr Endocrinol Metab 2023; 36:761-771. [PMID: 37440674 DOI: 10.1515/jpem-2023-0083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023] [Imported: 10/18/2023]
Abstract
OBJECTIVES To study the biochemical, clinical and molecular characteristics of 5,10- methylenetetrahydrofolate reductase (MTHFR) deficiency in Pakistani patients from a single center. METHODS Medical charts, urine organic acid chromatograms, plasma methionine and Hcys levels, and molecular testing results of MTHFR gene of patients presenting at the Biochemical Genetics Clinic, AKUH from 2016 to 2022 were reviewed. RESULTS Neonatal MTHFR deficiency was found in five patients. The median (IQR) age of symptom onset and diagnosis were 18 (8.5-22) and 26 (16.5-31) days. The median lag between symptom onset and diagnosis was 8 (4.5-12.5) days. The median age of treatment initiation and duration of treatment were 26 (16.5-49) and 32 (25.5-54) days. The most common clinical features were lethargy, poor feeding, and seizures. The MTHFR gene sequencing revealed homozygous variants p.K510K, p.R567*, and p.R157W. Renal insufficiency manifesting as elevated serum creatinine and responding to betaine therapy was noted in one patient. This has not been previously reported in neonatal MTHFR deficiency and may reflect engagement of alternate pathways of remethylation. Adult onset MTHFR deficiency was found in six patients, with a heterogeneous neurological presentation. The median lag between symptoms onset and diagnosis was 7 (3-11) years. MTHFR gene sequencing revealed homozygous variant p.A195V in five patients from one family and p.G261V in the other. Two of the five reported variants are novel that include p.R157W and p.G261V. CONCLUSIONS Eleven patients of this rare disorder from a single center indicate the need for clinical awareness and appropriate biochemical evaluation to ensure optimal outcomes.
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Ahmed S, Yaqub S, Siddiqui A, Jafri L. An Evaluation of the new 2021 Creatinine-Based Equation for Estimating Glomerular Filtration Rate (eGFR) in Pakistanis. Clin Lab 2023; 69. [PMID: 37560873 DOI: 10.7754/clin.lab.2023.230105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023] [Imported: 10/18/2023]
Abstract
BACKGROUND The new eGFR equation without race coefficients was recently developed and published by the CKD-EPI Collaboration. The new equation termed CKD-EPI 2021 has been endorsed by the National Kidney Foundation and the American Society of Nephrology. It is important to understand the impact this new equation might have on clinical decision making in practice; hence, this study is planned to evaluate the CKD-EPI 2021 equation in Pakistani population. To evaluate the performance of CKD-EPI 2021, CKD-EPI 2009, CKD-EPI Pak, and MDRD equations taking CrCl as gold standard. METHODS This retrospective cross-sectional study was conducted at the section of Chemical Pathology, Department of Pathology and Laboratory Medicine, in collaboration with section of Nephrology, Department of Medicine, Aga Khan University, Karachi. Consecutive laboratory results of subjects above 18 years; tested for CrCl or three months December 2021 to February 2022 was retrieved from the integrated laboratory management system (iLMS). Demographic details including gender and age alongside biochemical results of CrCl and serum Cr were recorded on a prestructured questionnaire. Statistical analysis of the data will be performed using Statistical Package of Social Sciences (SPSS) version 22. RESULTS After excluding those below 18 years of age, 2,609 cases were included in the final data analysis, with 1,419 (54.4%) males and 1,190 (45.6%) females. Mean age of the group was 52.8 ± 14.9 years. Among the 4 formulae tested against CrCl, CKD-EPI Pak showed the strongest correlation (r2 = 0.83), highest sensitivity 93.2% and negative predictive value of 93.0% with an overall agreement of 88%. CONCLUSIONS The CKD-EPI Pak equation is more accurate and precise in estimating GFR in Pakistani population. Based on the successful five years of experience of reporting eGFR using this equation by a large tertiary care hospital in Pakistan, this is high time to propagate its incorporation reflexly with SCr laboratory reports with no additional cost constraints.
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Jafri L, Ahmed S, Majid H, Ghani F, Pillay T, Khan AH, Siddiqui I, Shakeel S, Ahmed S, Azeem S, Khan A. A framework for implementing best laboratory practices for non-integrated point of care tests in low resource settings. EJIFCC 2023; 34:110-122. [PMID: 37455843 PMCID: PMC10349313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/18/2023] [Imported: 10/18/2023]
Abstract
The method we respond to pandemics is still inadequate for dealing with the point of care testing (POCT) requirements of the next large epidemic. The proposed framework highlights the importance of having defined policies and procedures in place for non-integrated POCT to protect patient safety. In the absence of a pathology laboratory, this paradigm may help in the supply of diagnostic services to low-resource centers. A review of the literature was used to construct this POCT framework for non-integrated and/or unconnected devices. It also sought professional advice from the Chemical Pathology faculty, quality assurance laboratory experts and international POCT experts from the International Federation of Clinical Chemistry and Laboratory Medicine (IFCC). Our concept presents a comprehensive integrated and networked approach to POCT with direct and indirect clinical laboratory supervision, particularly for outpatient and inpatient care in low-resource health care settings.
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Mahmood SBZ, Majid H, Arshad A, Niazali N, Kazi K, Aslam A, Ahmed S, Jamil B, Jafri L. Interleukin-6 (IL-6) as a Predictor of Clinical Outcomes in Patients with COVID-19. Clin Lab 2023; 69. [PMID: 37307132 DOI: 10.7754/clin.lab.2022.220741] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023] [Imported: 10/18/2023]
Abstract
BACKGROUND Interleukin-6 (IL-6) has been known to be involved in immune regulation, inflammatory response, and metabolism. It is also recognized as the major cause to underscore the pathology of severe COVID-19 patients. However, it remains to be seen if IL-6 is superior to other inflammatory biomarkers in ascertaining clinical severity and mortality rate for COVID-19. This study aimed to determine the value of IL-6 as a predictor of severity and mortality in COVID-19 patients and compare it with other pro-inflammatory biomarkers in the South Asian region. METHODS An observational study was conducted, including all adult SARS-CoV-2 patients who had undergone IL-6 testing from December 2020 to June 2021. The patients' medical records were reviewed to collect demographic, clinical, and biochemical data. Other pro-inflammatory biomarkers apart from IL-6 included Neutrophils to Lymphocyte Ratio (NLR), D-dimer, C-reactive protein (CRP), ferritin, lactate dehydrogenase (LDH), and procal-citonin for analysis. SPSS version 22.0 was utilized. RESULTS Out of the 393 patients who underwent IL-6 testing, 203 were included in the final analysis with a mean (SD) age of 61.9 years (12.9) and 70.9% (n = 144) were male. Fifty-six percent (n = 115) subjects had critical disease. IL-6 levels were elevated (> 7 pg/mL) in 160 (78.8%) patients. Levels of IL-6 significantly correlated with age, NLR, D-dimer, CRP, ferritin, LDH, length of stay, clinical severity, and mortality. All the inflammatory markers were significantly increased in critically ill and expired patients (p < 0.05). The receiver operator curve showed that IL-6 had the best area under the curve (0.898) compared to other pro-inflammatory biomarkers for mortality with comparable results for clinical severity. CONCLUSIONS Study findings show that though IL-6 is an effective marker of inflammation and can be helpful for clinicians in recognizing patients with severe COVID-19. However, we still need further studies with larger sample size.
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Nadeem S, Pervez A, Abid MA, Khalid RN, Rizvi NA, Aamdani SS, Ayub B, Mustafa MA, Ahmed S, Riaz M, Irfan K, Noordin S, Jafri L, Majid H, Umer M, Zehra N, Sheikh A, Haider AH, Khan AH. GRADE-ADOLOPMENT of clinical practice guideline for postmenopausal osteoporosis management-a Pakistani context. Arch Osteoporos 2023; 18:71. [PMID: 37204537 DOI: 10.1007/s11657-023-01258-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 04/25/2023] [Indexed: 05/20/2023] [Imported: 10/18/2023]
Abstract
Due to its high prevalence, we aimed to create postmenopausal osteoporosis clinical practice guideline via GRADE-ADOLOPMENT for Pakistan. We recommend a higher dose (2000-4000 IU) of vitamin D for osteoporotic patients who are old, have malabsorption, or are obese. The guideline will help standardize care provision and improve health care outcomes for osteoporosis. PURPOSE Postmenopausal osteoporosis affects one in every five postmenopausal women in Pakistan. An evidence-based clinical practice guideline (CPG) is needed to standardize care provision to optimize health outcomes. Hence, we aimed to develop CPG for the management of postmenopausal osteoporosis in Pakistan. METHODS The GRADE-ADOLOPMENT process was used to adopt (as is or with minor changes), exclude (omit), or adapt (modify based on local context) recommendations to the source guideline (SG)-clinical practice guidelines for the diagnosis and treatment of postmenopausal osteoporosis-2020 update from American Association of Clinical Endocrinology (AACE). RESULTS The SG was "adoloped" to cater to the local context. The SG consisted of 51 recommendations. Forty-five recommendations were adopted as is. Due to unavailability of drugs, 4 recommendations were adopted with minor changes, and one was excluded, while one recommendation was adopted with the inclusion of use of a surrogate FRAX tool specific for Pakistan. One recommendation regarding vitamin D dosage was adapted to recommend a dose of 2000-4000 IU of vitamin D in patients with obesity, malabsorption, and old age. CONCLUSION The developed Pakistani postmenopausal osteoporosis guideline consists of 50 recommendations. The guideline created recommends a higher dose (2000-4000 IU) of vitamin D for patients who are old, have malabsorption, or are obese, which is an adaptation from the SG by the AACE. This higher dose is justified as lower doses prove to be suboptimal in these groups and should be complemented with baseline vitamin D and calcium levels.
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Ahmed S, Siddiqui A, DeBerardinis RJ, Ni M, Gu W, Cai F, Vu H, Afroze B. L-2 hydroxyglutaric aciduria- review of literature & case series. Ann Med Surg (Lond) 2023; 85:712-717. [PMID: 37113859 PMCID: PMC10129278 DOI: 10.1097/ms9.0000000000000326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 02/23/2023] [Indexed: 04/05/2023] [Imported: 10/18/2023] Open
Abstract
L-2-hydroxyglutaric aciduria (L2HGA) is an autosomal recessive, slowly progressive neurodegenerative disease characterized by psychomotor delay and cerebellar dysfunction. The biochemical hallmark is increased concentrations of L2HG in body fluids. Brain MRI exhibits characteristic centripetal extension of the white matter involvement that differentiates it from other leukodystrophies. The authors report two sisters from Pakistan with L2HGA with 4 years of follow-up. The authors have also compared the clinical outcome of our patients with 45 previously reported patients with L2HGA for whom treatment and clinical outcome was reported. Case presentation The authors report two sisters with L2HGA from Pakistan born to consanguineous parents. The 15- and 17-year-old girls presented with psychomotor delay, seizures, ataxia, intentional tremors, and dysarthria. Both had normal anthropometric measurements for age. Exaggerated tendon reflexes and bilateral sustained ankle clonus were observed in addition to cerebellar signs. Urine organic acids analysis showed marked excretion of 2-hydroxyglutaric acid, chiral differentiation of 2-hydroxyglutaric acid showed it to be L2HGA. Brain MRI of the 15-year-old showed diffuse subcortical white matter changes evident by T2/FLAIR hyperintense signals bilaterally, particularly in the frontal region in the centripetal distribution with some diffusion restriction along involvement of globus pallidus. The characteristic MRI pattern raised the suspicion of L2HGA. Targeted L2HGDH sequencing identified a homozygous pathogenic variant, c.829C>T (p.Arg227*) in L2HGDH gene in both girls. Both parents were heterozygous carriers of the familial variant. Conclusion Neuroradiological features of centripetal subcortical leukoencephalopathy with basal ganglia and dentate nuclei involvement are rather specific to L2HGA and should lead to further biochemical investigations to look for L2HGA and L2HGDH gene sequencing.
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Data mining for prothrombin time and international normalized ratio reference intervals in children. PLoS One 2022; 17:e0276884. [PMID: 36302050 PMCID: PMC9612453 DOI: 10.1371/journal.pone.0276884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 10/13/2022] [Indexed: 11/14/2022] [Imported: 10/18/2023] Open
Abstract
Reference intervals (RIs) help physicians in differentiating healthy from sick individuals. The prothrombin time (PT) and International normalized ratio (INR) fluctuate in coagulation pathway defects and have interlaboratory variability due to the instrument/reagent used. As direct method is difficult in children, we chose an indirect data mining method for the determining PT/INR RIs. The indirect method overcomes the substantial financial and logistic challenges, and ethical restrictions in children, moreover, allows partitioning in more fine-grained age groups. Prothrombin Time/INR measurements performed in patients aged birth-18 years between January 2013 and December 2020, were retrieved from laboratory management system of the Aga Khan Hospital. Reference intervals were computed using an indirect KOSMIC algorithm. The KOSMIC package function on the assumption that the non-pathologic samples follow a Gaussian distribution (after Box-Cox transformation of the data), following an elaborate statistical process to isolate distribution of physiological samples from mixed dataset. A total of 56,712 and 52,245 values were retrieved for PT and INR respectively. After the exclusion of patients with multiple specimens obtained during the study period, RIs were calculated for 37,356 (PT) and 37,192 (INR) children with stratification into 9 age groups. A comparison of 2.5th and 97.5th percentile results with those of established RIs from SickKids Handbook of Pediatric Thrombosis and Hemostasis demonstrated good agreement in between different age groups. This study supports data mining as an alternate approach for establishing PT/INR RIs, specifically in resource-limited settings. The results obtained are specific to studied population and instrument/reagent used. The study also allows understanding of fluctuations in coagulation pathways with increasing age and hence better clinical decision-making based on PT and INR results.
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Ahmed S, Abbas AM, Jahan F, Ozben T. Virtual assessment, training, and evaluation of clinical laboratory technologists amidst peak Covid-19 pandemic: An observational study. J Med Biochem 2022; 41:559-563. [PMID: 36381081 PMCID: PMC9618329 DOI: 10.5937/jomb0-33962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 01/24/2022] [Indexed: 08/29/2023] [Imported: 08/29/2023] Open
Abstract
Medical technologists are considered a neglected group when it comes to academic interventions. We developed and implemented an educational intervention and assessment for the technologists based on an online questionnaire as a pre-test consisting of questions related to knowledge (n=5), attitude (n=3), and practices (n=4) of daily internal quality control (QC) monitoring via Google Docs survey tool. This study served multiple purposes. It allowed keeping the technologists engaged during the peak of the COVID-19 pandemic while also improving the knowledge, attitude, and practices about the internal quality control using Bio-Rad Unity Real Time (URT) QC software. Subjects were graded based on the scores they received out of 100 (0-60 = poor; 61-79 = good; 80-100 = excellent). Training materials, i.e., a set of 5 videos every week via e-mail, were circulated. A voice-over PowerPoint presentation was also shared for easy comprehension. This activity was repeated after one month. A post-test was administered to assess the improvement. The study results show significant improvement in the technologists' performance after the intervention.
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Abid MA, Ahmed S, Muneer S, Khan S, de Oliveira MHS, Kausar R, Siddiqui I. Evaluation of CSF kappa free light chains for the diagnosis of multiple sclerosis (MS): a comparison with oligoclonal bands (OCB) detection via isoelectric focusing (IEF) coupled with immunoblotting. J Clin Pathol 2022; 76:353-356. [PMID: 36130824 PMCID: PMC10176397 DOI: 10.1136/jcp-2022-208354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 09/15/2022] [Indexed: 11/03/2022] [Imported: 08/29/2023]
Abstract
This study was done to evaluate the diagnostic accuracy of cerebrospinal fluid kappa free light chain (KFLC) for diagnosis of multiple sclerosis, against isoelectrofocusing (IEF) to detect oligoclonal bands (OCB) as gold standard. 64 cases were divided into positive and negative based on the OCB results. Diagnostic accuracy was calculated for the 1 mg/L cut-off. The 1 mg/L cut-off yielded a percent agreement of 86.1% and Cohen's kappa value of 0.8. Youden's index, yielded a cut-off of 0.92 mg/L as optimal (90.3% specificity and 90.9% sensitivity). The analytical time was 3 hours and 55 min for IEF and 25 min for KFLC. The cost of a single OCB test was PKR12 000 (US$68.17) compared with PKR4150 (US$23.58) for KFLC. KFLC proved to be an accurate, cheaper and time-saving alternative and can be performed prior to the contemporary testing.
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Khan ZUN, Jafri L, Hall PL, Schultz MJ, Ahmed S, Khan AH, Majid H. Utilizing augmented artificial intelligence for aminoacidopathies using collaborative laboratory integrated reporting- A cross-sectional study. Ann Med Surg (Lond) 2022; 82:104651. [PMID: 36268324 PMCID: PMC9577660 DOI: 10.1016/j.amsu.2022.104651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/05/2022] [Accepted: 09/10/2022] [Indexed: 11/27/2022] [Imported: 10/18/2023] Open
Abstract
Introduction Plasma amino acids profiling can aid in the screening and diagnosis of aminoacidopathies. The goal of the current study was to analyze and report the metabolic profiles of plasma amino acid (PAA) and additionally to compare PAA-reference intervals (RI) from Pakistan with more countries utilizing Clinical Laboratory Integrated Reports (CLIR). Methods This was a cross sectional prospective single center study. Twenty-two amino acids were analyzed in each sample received for one year at the clinical laboratory. Data was divided into reference and case data files after interpretation by a team of pathologists and technologists. All PAA samples were analyzed using ion-exchange high-performance chromatography. The CLIR application of Amino Acid in Plasma (AAQP) was used for statistical analysis for both data sets and post-analytical interpretive tools using a single condition tool was applied. Result The majority of 92% (n = 1913) of PAA profiles out of the total 2081 tests run were non-diagnostic; the PAA values were within the age-specific RI. The PAA median was in close comparison close to the 50th percentile of reference data available in CLIR software. Out of the total 2081 tests run, one hundred and sixty-eight had abnormal PAA levels; 27.38% were labeled as non-fasting samples, and the main aminoacidopathies identified were Phenylketonuria and Maple Syrup Urine Disorder. Conclusion An agreement of >95% was observed between the reporting done by the pathologists and technologists’ team and then after the application of CLIR. Augmented artificial intelligence using CLIR can improve the accuracy of reporting rare aminoacidopathies in a developing country like ours. Plasma amino acids helps in diagnosing and monitoring of various aminoacidopathies. Few aminoacidopathies present with a grossly abnormal investigation profile, with few diseases having subtle deviations. Their is 98% concordance of diagnosis concordance of diagnosis of aminoacidopathies between our lab and CLIR. CLIR tools can be utilized in a newborn screening program for screening and diagnosis in future.
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Majid H, Jafri L, Ahmed S, Abid MA, Aamir M, Ijaz A, Khan AH, Siddiqui I. Publication dynamics: what can be done to eliminate barriers to publishing full manuscripts by the postgraduate trainees of a low-middle income country? BMC Res Notes 2022; 15:249. [PMID: 35841067 PMCID: PMC9284783 DOI: 10.1186/s13104-022-06138-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 06/30/2022] [Indexed: 11/10/2022] [Imported: 10/18/2023] Open
Abstract
OBJECTIVES This study aimed to determine the publication rate of free paper abstracts presented by the postgraduate (PG) trainees and determine the reasons for non-publication. A mixed methods study was conducted. PG trainees presenting free papers at the at the Pakistan Society of Chemical Pathologist conferences from 2012 to 2018 were included. Three databases were searched to identify if the abstracts were published or not. The PG trainee authors of abstracts not published as full manuscript, were surveyed to determine the barriers and challenges in publishing a manuscript. RESULTS The average rate of full manuscript publication was 51.8% (n = 93/177) for the abstracts presented by the PG trainees. Publication rate was higher for oral (n = 73/119, 61.3%) compared to poster presentation (n = 20/58, 34.5%). Most of the manuscripts were published after two years of abstract presentation. The survey showed that the main challenges to publishing an abstract were lack of time, limited scientific writing or submission skills, lack of funding for publication fee, and negative or statistically non-significant results. This reflects a need to arrange workshops/symposia for the PG trainees of low-middle income country (LMIC) to enhance their writing and time management skills and improve the full manuscript publication rate from LMICs.
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Hashmi SB, Ahmed S. Children with lysinuric protein intolerance: Experience from a lower middle income country. World J Clin Pediatr 2022; 11:369-374. [PMID: 36052112 PMCID: PMC9331405 DOI: 10.5409/wjcp.v11.i4.369] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 03/21/2022] [Accepted: 06/03/2022] [Indexed: 02/06/2023] [Imported: 08/29/2023] Open
Abstract
BACKGROUND Lysinuric protein intolerance (LPI) is an inborn error of metabolism consequential to recessive mutations in the SLC7A7 gene. The metabolic imbalance in absorption and excretion of dibasic amino acids is considered the basis of LPI. The disease results from protein intolerance with signs and symptoms oscillating from cerebral impairment, respiratory involvement, renal failure and autoimmune complications.
AIM To determine biochemical and clinical presentation of cases with biochemical picture suggestive of LPI in Pakistani children.
METHODS The study was conducted at the Biochemical Genetic Lab, Department of Pathology and Laboratory Medicine, AKU Plasma, and urine amino acid quantification data from January 2013 to October 2018 was included in this study. The amino acids were analyzed by high performance liquid chromatography. Prestructured requisition forms were used to obtain the clinicopathological data. Statistical analysis was done by Microsoft Excel 2017.
RESULTS A total of 6 patients were recognized. All the patients were male (100%). The mean age was 24 mo ± 10 d. All the patients had low plasma concentration of lysine, ornithine and arginine, whereas increased levels of lysine, ornithine and arginine in urine were observed in 2 patients. History of consanguineous marriage was present in all patients (100%). The most observed clinical symptom was feeding difficulty followed by failure to thrive (83.3%) and developmental delay (66.6%). Hepatomegaly was present in all patients (100%). No mutation analysis was done.
CONCLUSION This study portrays the biochemical and clinical spectrum of LPI in Pakistan. Although clinical manifestations appeared in the first 2 years of life, most of them suffered a delay in undergoing diagnostic workup.
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Ahmed S, Zierk J, Khan AH, Jafri L, Majid H, Ghani F, Siddiqui I. Reference Intervals of Serum TSH from Mixed Distributions Using Truncation Points and the Kolmogorov-Smirnov Distance. Clin Lab 2022; 68. [PMID: 35975518 DOI: 10.7754/clin.lab.2021.210833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023] [Imported: 10/18/2023]
Abstract
BACKGROUND Serum TSH reference intervals (RIs) are methodology, population, and age specific. However, the ethical and practical challenges restrict the establishment of pediatric RIs using conventional approaches and advocates the use of indirect data mining-based algorithms. This study was carried out to estimate the reference interval of neonatal serum TSH in Pakistani population using an indirect approach. METHODS A data mining of serum TSH results of neonates (≤ 1 month of age) from 2013 - 2018 was done. Two subgroups on the basis of age from birth to 5 days and 6 - 30 days were assessed. The German study group's pre-validated indirect algorithm 'KOSMIC' was utilized for the statistical analysis. RESULTS A total of non-duplicate 82,299 neonatal serum TSH tests were retrieved over a period of 6 years, including 88% (n = 70,788) aged 0 - 5 days and 12% (n = 11,511) ranging from 6 days to 1 month. The estimated RIs for the first age partition was 0.7 (90% CI 0.6 - 0.8) to 15.5 (90% CI 12.9 - 16.2) and for the second group 0.7 (90% CI 0.5 - 0.9) to 7.8 (90% CI 6.1 - 9.9) µIU/mL. CONCLUSIONS This study revealed age related trends in serum TSH. The study advocates the need for population specific RIs owing to the significant variations noted on comparison with previously published literature. Precise RIs become vital particularly when serum TSH is undertaken as a confirmatory test for presumptive positive results on newborn screening for congenital hypothyroidism.
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Majid H, Ahmed S, Muneer S, Hamid R, Jafri L, Khan AH. Biotin-responsive Multiple Carboxylase Deficiency (MCD). J Coll Physicians Surg Pak 2022; 32:823-825. [PMID: 35686422 DOI: 10.29271/jcpsp.2022.06.823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 03/09/2022] [Indexed: 06/15/2023] [Imported: 10/18/2023]
Abstract
This study aimed to determine the clinical spectrum and biochemical findings on urine organic acids (UOA) in Biotin-responsive multiple carboxylase deficiency (MCD) patients presenting to the biochemical genetics laboratory (BGL). Patients reported as MCD, from January 2013-December 2020 were included. The UOA was analysed by gas chromatography mass spectrometer. Demographic, clinical, and biochemical details were extracted from the BGL history form. Two hundred and two patients were reported to have biotin responsive MCD with 111(55%) males and a median (Q3-Q1) age of 7 months (13-4). Of these 71.7% (n=145) patients presented in infantile period. Parental consanguinity was observed in 80% (n=161) and another 32.6% (n=66) cases grandparents were cousins. The main presenting features were seizures, developmental delay, and lethargy. The common peaks were determined on UOA 3OHIVA, MC and MCC. MCD is not rare in Pakistani population; it is recommended to include this disorder in newborn screening programs. Key Words: Biotin responsive multiple carboxylase deficiency, Organic acids, Amino acids, Pakistan, Inborn errors of metabolism.
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Jafri L, Abid MA, Rehman J, Ahmed S, Abbas G, Ali H, Kanani F, Ali U, Alavi N, Aslam F, Iqbal S, Ijaz A, Munir MU, Dildar S, Nawaz SH, Adnan K, Khan AH, Zubairi AM, Siddiqui I. Development of a virtual classroom for pre-analytical phase of laboratory medicine for undergraduate medical students using the Delphi technique. PLoS One 2022; 17:e0264447. [PMID: 35385486 PMCID: PMC8985926 DOI: 10.1371/journal.pone.0264447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 02/10/2022] [Indexed: 11/19/2022] [Imported: 10/18/2023] Open
Abstract
Background Amongst the pre-analytical, analytical, and post-analytical phase of laboratory testing, pre-analytical phase is the most error-prone. Knowledge gaps in understanding of pre-analytical factors are identified in the clinical years amongst undergraduate students due to lack of formal teaching modules on the pre-analytical phase. This study was conducted to seek experts’ consensus in Clinical Chemistry on learning objectives and contents using the Delphi technique with an aim to develop an asynchronous virtual classroom for teaching pre-analytical factors of laboratory testing. Methods A mixed method study was conducted at the Aga Khan University. A questionnaire comprising of 16 learning objectives and their associated triggers was developed on Google Docs for developing the case vignettes. A four-point Likert Scale, which included strongly agree, agree, disagree and strongly disagree, was utilized for the learning objectives. An open-ended question was included for experts to suggest new items for inclusion. A cut off of at least 75% agreement was set to establish consensus on each item. A total of 17 Chemical Pathology faculty from 13 institutions across Pakistan were invited to participate in the first round of Delphi. Similar method of response was used in round two to establish consensus on the newly identified items suggested by the faculty in round 1. Later, the agreed-upon objectives and triggers were used to develop interactive scenarios over Moodle to concurrently test and teach medical students in a nonchalant manner. Results A total of 17 responses were received in Round 1 of the Delphi process (response rate = 100%), while 12 responses were received in Round 2 (response rate = 71%). In round 1, all 16 learning objectives reached the required consensus (≥ 75%) with no additional learning objectives suggested by the experts. Out of 75 triggers in round 1, 61 (81.3%) reached the consensus to be included while 39 were additionally suggested. In 2nd round, 17 out of 39 newly suggested triggers met the desired consensus. 14 triggers did not reach the consensus after two rounds, and were therefore eliminated. The virtual classroom developed using the agreed-upon learning objectives and triggers consisted of 20 items with a total score of 31 marks. The questions included multiple choice questions, fill in the blanks, drag and drop sequences and read-and-answer comprehensions. Specific learning points were included after each item and graphs and pictures were included for a vibrant experience. Conclusion We developed an effective and interactive virtual session with expert consensus on the pre-analytical phase of laboratory testing for undergraduate medical students which can be used for medical technologist, graduate students and fellows in Chemical Pathology.
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Ahmed S, Akbar F, Ali AJ, Afroze B. Clinical, pathological and molecular spectrum of patients with glycogen storage diseases in Pakistan. J Pediatr Endocrinol Metab 2022; 35:373-385. [PMID: 34989216 DOI: 10.1515/jpem-2021-0575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 12/20/2021] [Indexed: 11/15/2022] [Imported: 10/18/2023]
Abstract
OBJECTIVES Evaluation of clinical, biochemical and molecular analysis of Pakistani patients with hepatic GSDs. METHODS Medical charts, biochemical, histopathological and molecular results of patients with hepatic GSD were reviewed. RESULTS Out of 55 GSD patients, 41 (74.5%) were males and 14 (25.5%) were females with consanguinity in 50 (91%) patients. The median age of initial symptoms, clinic diagnosis and molecular diagnosis were 450 (IQR: 270-960), 1,095 (IQR: 510-1,825) and 1717 (IQR: 796-3,011) days, respectively. Molecular analysis and enzyme activity was available for 33 (60%) and two patients, respectively. GSD III (n=9) was most prevalent followed by GSD Ib (n=7), GSD IXc (n=6), GSD VI (n=4), GSD Ia (n=3), GSD XI (n=3), GSD IXb (n=2) and GSD IXa (n=1). In patients (n=33) who underwent molecular analysis; 19 different variants in eight genes associated with GSD were identified. We also report five novel variants, two in SLC37A4, one in AGL and two in PYGL contributing to the diagnosis of GSD Ib, GSD III and GSD VI, respectively. CONCLUSIONS Fifty-five patients of GSDs in 26 families from a single care provider indicate a relatively high frequency of GSD in Pakistan, with multiple unrelated families harboring identical disease-causing variants, on molecular analysis, including two known pathogenic variants in SLC37A4 and PHKG2, and a novel variant in AGL.
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Jafri L, Abid MA, Asif H, Hashmi B, Majid H, Ghani F, Ahmed S, Siddiqui I, Khan AH. Development and validation of standard and real patient gallstone library using Fourier transform infra-red spectroscopy. BMC Gastroenterol 2022; 22:146. [PMID: 35346074 PMCID: PMC8962173 DOI: 10.1186/s12876-022-02227-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 03/14/2022] [Indexed: 02/15/2023] [Imported: 10/18/2023] Open
Abstract
Background Analysis of the constituents of gallstones using various spectroscopic techniques assists in identification of the pathogenesis of gallstones. In the current study, using Fourier Transform Infra-Red (FTIR) Spectroscopy, a Gallstone Standard Library (GSL) and a Gallstone Real Patients’ Library (GRPL) were developed and validated for gallstone composition analysis. Methods The study was conducted at the Department of Pathology & Laboratory Medicine, Aga Khan University, Pakistan. Pure standards (cholesterol, calcium carbonate, bilirubin and bile salts) and gallstone specimens were analyzed using FTIR Nicolet iS-5 Spectrometer from Thermo Fisher Scientific, USA. Thermo Scientific™ QCheck™ algorithm, embedded within the OMNIC™ software, was used to identify the unique spectral fingerprint of the patient samples to match with known, standard material. Matching of > 75% was considered acceptable. Validation for accuracy of the library was performed for twenty analyzed gallstones at an international reference lab. Results Concerted search analysis was performed against the developed GSL consisting of 71 “pure component” spectrum divided into 5 types to generate the library. For the Gallstone Real Patient Library (GRPL), 117 patient samples were analyzed. Ninety-eight gall stones (83.8%) out of 117 stones matched with the developed GSL. Majority stones were mixed stones (95.92%), with cholesterol being the primary component (91.83%). Results of the developed library were 100% in agreement with the reports received from the external reference lab. Conclusions The library developed displayed good consistency and can be used for detection of gallstone composition in Pakistan and replace the traditional labor- and time-intensive chemical method of gallstone analysis.
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Khan ZUN, Chand P, Majid H, Ahmed S, Khan AH, Jamil A, Ejaz S, Wasim A, Khan KA, Jafri L. Urinary metabolomics using gas chromatography-mass spectrometry: potential biomarkers for autism spectrum disorder. BMC Neurol 2022; 22:101. [PMID: 35300604 PMCID: PMC8932302 DOI: 10.1186/s12883-022-02630-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 03/07/2022] [Indexed: 11/29/2022] [Imported: 10/18/2023] Open
Abstract
Background Diagnosis of autism spectrum disorder (ASD) is generally made phenotypically and the hunt for ASD-biomarkers continues. The purpose of this study was to compare urine organic acids profiles of ASD versus typically developing (TD) children to identify potential biomarkers for diagnosis and exploration of ASD etiology. Methods This case control study was performed in the Department of Pathology and Laboratory Medicine in collaboration with the Department of Pediatrics and Child Health, Aga Khan University, Pakistan. Midstream urine was collected in the first half of the day time before noon from the children with ASD diagnosed by a pediatric neurologist based on DSM-5 criteria and TD healthy controls from August 2019 to June 2021. The urine organic acids were analyzed by Gas Chromatography-Mass Spectrometry. To identify potential biomarkers for ASD canonical linear discriminant analysis was carried out for the organic acids, quantified in comparison to an internal standard. Results A total of 85 subjects were enrolled in the current study. The mean age of the ASD (n = 65) and TD groups (n = 20) was 4.5 ± 2.3 and 6.4 ± 2.2 years respectively with 72.3% males in the ASD group and 50% males in the TD group. Parental consanguinity was 47.7 and 30% in ASD and TD groups, respectively. The common clinical signs noted in children with ASD were developmental delay (70.8%), delayed language skills (66.2%), and inability to articulate sentences (56.9%). Discriminant analysis showed that 3-hydroxyisovalericc, homovanillic acid, adipic acid, suberic acid, and indole acetic were significantly different between ASD and TD groups. The biochemical classification results reveal that 88.2% of cases were classified correctly into ASD& TD groups based on the urine organic acid profiles. Conclusion 3-hydroxy isovaleric acid, homovanillic acid, adipic acid, suberic acid, and indole acetic were good discriminators between the two groups. The discovered potential biomarkers could be valuable for future research in children with ASD.
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Ahmed S, Jafri L. Reflex Reporting of Estimated Glomerular Filtration Rate (eGFR) with Serum Creatinine: A Win-win Situation for both Patients and Physicians. J Coll Physicians Surg Pak 2022; 32:411. [PMID: 35148606 DOI: 10.29271/jcpsp.2022.03.411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/20/2021] [Indexed: 06/14/2023] [Imported: 10/18/2023]
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Majid H, Jafri L, Ahmed S, Humayun K, Kirmani S, Ali N, Moiz B, Khan AH, Afroze B. Perspective on newborn screening (NBS): evidence sharing on conditions to be included in NBS in Pakistan. J PAK MED ASSOC 2022; 72:526-531. [PMID: 35320237 DOI: 10.47391/jpma.01181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] [Imported: 10/18/2023]
Abstract
Abstract
Newborn screening aims at detecting treatable disorders early so that the treatment can be initiated to prevent mortality and morbidity. Such programmes are well established in most developed countries, and all newborns are screened for selected metabolic, endocrine and other disorders based on disease epidemiology, testing and treatment availability, efficiency and cost-effectiveness. Even in developing countries, such screening programmes are initiated using heel prick capillary blood collected on filter paper. The current narrative was planned to provide a perspective with evidence in favour of starting newborn screened for different disorders. The programme project should be initiated nationwide, taking one disorder, congenital hypothyroidism, as the prototype and a newborn screening panel can then be extended to include other disorders. A task force should be set up to recommend disorders to be included in the panel, develop the national plan policies, and define procedures to strengthen the testing.
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Ahmed S, Abid MA, Olivera MHSD, Jafri L, Ahmed ZA, Siddiqui I. Forecasting COVID-19 Testing Load Using Google Trends: Experience from a Lower Middle-Income Country with over 10 Million Diagnostic Tests. Clin Lab 2022; 68. [PMID: 35142199 DOI: 10.7754/clin.lab.2021.210613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] [Imported: 10/18/2023]
Abstract
BACKGROUND The ability to forecast changing trends of COVID-19 can help drive efforts to sustain the increasing burden on the healthcare system, specifically the clinical laboratories. We aimed to assess whether the trends of SARS-CoV-2 testing in Pakistan can be predicted using COVID-19 symptoms as search terms and analyzing the data from Google Trends. METHODS The number of weekly SARS-CoV-2 tests performed were retrieved from online COVID-19 data resource. Google Trends data for the search terms with most common COVID-19 symptoms was analyzed for cross-correlation with the number of tests performed nationally. RESULTS A total of 10,066,255 SARS-CoV-2 diagnostic tests were analyzed. Search terms of fever, headache, and shortness of breath displayed a statistically significant correlation with total number of tests performed with a 1-week time lag. CONCLUSIONS Google Trends data can be used to forecast the changing trends in COVID-19 testing. This information can be used for careful planning and arrangements to meet increased diagnostic and healthcare demands in difficult times.
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Ahmed S, Ahmed ZA, Rashid NH, Mansoor M, Siddiqui I, Jafri L. Procalcitonin as a predictor of severity and mortality in a cohort of patients hospitalised with COVID-19. THE MALAYSIAN JOURNAL OF PATHOLOGY 2021; 43:375-380. [PMID: 34958058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/14/2023] [Imported: 10/18/2023]
Abstract
INTRODUCTION To evaluate the association of Procalcitonin (PCT) with severity in Coronavirus disease 2019 (COVID-19), hospitalised patients and to test the hypothesis that it is an independent predictor of mortality. MATERIALS AND METHODS This study was conducted at Chemical Pathology, Department of Pathology and Laboratory Medicine and Department of Medicine, Aga Khan University (AKU), Karachi Pakistan. Electronic medical records of all in-patients including both genders and all age groups with documented COVID-19 from March to August 2020 were reviewed and recorded on a pre-structured performa. The subjects were divided into two categories severe and non-severe COVID-19; and survivors and non-survivors. Between-group differences were tested using the Chi-square and Mann-Whitney's U-test. The receiver operating characteristic curve was plotted for serum PCT with severity and mortality. A binary logistic regression was used to identify variables independently associated with mortality. The data was analysed using SPSS. RESULTS 336 patients were reviewed as declared COVID-19 positive during the study duration, and 136 were included in the final analysis including 101 males and 35 females. A statistically significant difference in PCT was found between severe and non-severe COVID-19 (p value=0.01); and survivors and nonsurvivors (p value<0.0001). PCT, older age and increased duration of hospital stay were revealed as variables independently associated with mortality. On ROC analysis, an AUC of 0.76 for mortality prediction was generated for PCT. CONCLUSION Baseline serum PCT concentration is a promising predictor of mortality and severity in COVID-19 cases when considered in combination with clinical details and other laboratory tests.
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