Genomics of Acute Myeloid Leukemia

Acute myelogenous leukemia (AML) is a clonal, malignant disease of hematopoietic tissue that is characterized by accumulation of abnormal (leukemic) blast cells, principally in the bone marrow. Representation of these genetic mutations and the involvement patterns seems to follow specific and temporally ordered fluctuating manners. Somatic mutations in these genes are represented as a variety of recurrent chromosomal abnormalities, e.g., t (8;21), t(15;17), etc., or by the presence of prognostic markers, e.g., FLT3, MLL, NPM1 and CEBPA as well as encoding epigenetic modifiers, such as DNMT3A, ASXL1, TET2, IDH1, and IDH2, are commonly acquired early and are present in the founding clone. The same genes are frequently found to be mutated in elderly individuals along with clonal expansion of hematopoiesis that confers an increased risk for the development of hematologic cancers. Furthermore, such genomic changes may persist after therapy, lead to clonal expansion during hematologic remission, and eventually lead to relapsed disease. Majority of genetic data are now being used to classification, risk stratification, and clinical care of patients. The unprecedented molecular characterization provided by advanced and deeply sensitized molecular assays like next-generation sequencing (NGS) offers the potential for an individualized approach to treatment in AML, bringing us one step closer to personalized medicine

Assessment of WT1 expression as a marker of treatment outcome in karyotype normal acute myeloid leukemia patients in Pakistan

Currently, there is an effort to predict relapse by follow-up monitoring of MRD and subsequently to begin the treatment of the patients during their clinical and hematological remission prior to overt hematological relapse. Expression of WT1 in AM Lis known to be independently associated with significant inferior response to therapy and short survival outcome. Follow-up monitoring of WT1 gene expression during or after therapy would be a valuable predictive marker for early recurrence or relapse of AMLdisease. This pilot study evaluated newly diagnosed and post-induction or consolidation chemotherapy of AMLpatients who were registered with the Oncology Clinics of the Aga Khan University Hospital, Karachi. High WT1 burden (\u3e 5000 copies/ml) in 2 patients was indicative of early recurrence of the disease along with shorter disease-free and overall survival. Low WT1 expression (\u3c 200 copies/ml) in 2 patients after induction and consolidation therapy, respectively, was suggestive of better prognosis

A cross sectional evaluation of the corona-score for swift identification of SARS-CoV-2 infection at a tertiary care hospital in Pakistan

Background: The Corona-Score is one of the first and most widely used predictive model for coronavirus 2 (SARS-CoV-2) infection. The purpose of this study was to validate the performance of Corona-Score in a cohort of Pakistani patients pursuing care for suspected infection.Methods: After seeking institution\u27s ethical committee exemption, results of serum lactate dehydrogenase (LDH), C-reactive protein (CRP), ferritin, absolute lymphocyte and neutrophil counts, chest x-ray findings and demographics of suspected COVID-19 cases with respiratory symptoms were recouped from electronic medical record. The pre-validated score as proposed by Kurstjens S et al., was calculated. The subjects were divided into SARS-CoV-2 positive and negative on the basis of reverse transcription-polymerase chain reaction (RT-PCR) findings. Median and interquartile range (IQR) was calculated for the score in the two groups and the difference was assessed using the independent sample median test. Receiver operating characteristics (ROC) curve analysis was plotted. Statistical analyses were carried out using SPSS 26, with statistical significance set at p value \u3c 0.05.Results: A total of sixty cases, 30 (50%) RT-PCR positive and 30 (50%) negative with a median Corona-Score of 3.5 (IQR: 0-6) and 1.5 (IQR: 0-4) respectively, were evaluated. A p-value of 0.61 showing no statistically significant between group differences was observed. The area under the curve of Corona-Score in our population of patients was 0.59 (95% CI: 0.45-0.74). Using the cut-off values of four originally identified by Kurstjens et al. the model displayed 43.3% sensitivity and 70% specificity with an overall accuracy of 56.67%.Conclusion: Corona-Score displayed a lower diagnostic accuracy which may be attributable to the different genetic framework, viral strain and severity of the disease in Pakistanis compared to the population where this score was originally validated. However, large multi-center studies across the country are dire need of time to evaluate the score in overly exhausted health care setup and limited availability of PCR testing

Evaluation of serum ferritin for prediction of severity and mortality in COVID-19- A cross sectional study

Background: Ferritin even though widely recognized as a representative of total body iron stores, its prognostic utility is linked with COVID-19. This study was aimed at evaluation of the association of ferritin with severity in Coronavirus disease 2019 (COVID-19), hospitalized patients and to test the hypothesis that it is an independent predictor of mortality.Material and methods: This study was conducted at Chemical Pathology, Department of Pathology and Laboratory Medicine, Aga Khan University (AKU), Karachi. Medical records of all in-patients including both genders, and all age groups with documented COVID-19 from 1st March to 10th August 2020 were reviewed. The subjects were divided into two categories severe and non-severe COVID-19; and survivors and non-survivors. The details were recorded on a pre-structured performa. Between-group differences were tested using the Mann-Whitney\u27s U-test. The receiver operating characteristic curve was plotted for ferritin with severity and mortality. A binary logistic regression was used to identify variables independently associated with mortality. The data was analyzed using Statistical Package for the Social Sciences (SPSS).Results: A total of 336 in patients were reviewed as declared COVID-19 positive during the study duration, and 157 were included in the final analysis including 108 males and 49 females. Statistically significant difference in ferritin was found in the two categories based on severity and mortality. Binary logistic regression showed ferritin to be an independent predictor of all-cause mortality supplemented with an AUC of 0.69 on ROC analysis.Conclusions: Serum ferritin concentration is a promising predictor of mortality in COVID-19 cases

Therapeutic Targets and Signaling Pathways for Diagnosis of Myeloma

Multiple myeloma (MM) is a malignancy of plasma cells that not only shows different clinical behavior but also depicts heterogeneous groups at molecular level. The prognosis of the disease has been dramatically changed with the arrival of new drugs in the past few years. In this context of better therapeutic agents, there are important challenges for accurate evaluation of patients by better prognostic and predictive tools. Transcriptomic studies have largely added to decipher MM heterogeneity, dividing MM patients into different subgroups according to prognosis. Micro-arrays and more recently RNA sequencing have helped in evaluating coding and non-coding genes, mutations, unique transcriptome convertors and different splicing events giving new information concerning biology, outcome and treatment options. Initial data from gene expression profiling studies have also pointed out genes that predict prognosis, i.e., CSK1-B, and can deliver pharmacogenomics and biologic vision into the pathophysiology, targeted treatment, and future direction. Importantly, we suggest that all prospective studies and clinical trials now accept genetic testing and risk stratification of MM patients. In this review, we discuss the part and effect of gene expression profiling in myeloma

Clinico-pathological profile and outcomes of patients with polycythaemia vera, essential thrombocythaemia and idiopathic myelofibrosis: a tertiary care center experience from southern Pakistan

Background: The “Philadelphia Negative Classic Myeloproliferative Neoplasms” include polycythaemia vera (PV), essential thrombocythaemia (ET) andidiopathic myelofibrosis (IMF). These three disorders share several clinical and laboratory features including JAK2 V617F mutation. Our objectives were to determine the clinicoat hological profile and outcomes of Pakistani patients with polycythaemia vera (PV), essential thrombocythaemia (ET) and idiopathic myelofibrosis (IMF) in order to have an insight regarding behaviour of these conditions. Methods: A retrospective analysis of all the cases of PV, ET and IMF diagnosed at our institute from January 1995 to December 2013 was performed.Age, gender, clinical presentation, laboratory investigations, treatment provided and duration of follow up were included for analysis. Appropriatestatistics were utilized for calculation of data. Results: A total of 58 patients were diagnosed as PV, ET or IMF during the study period. Male to female ratio was 1.1:1Forty five percent (n=2) patients came to medical attention due to abnormal laboratory results, 3 had cerebrovascular events, 3 had pruritus, and 1 patient each with gangrene and BuddChiari syndrome. Haemorrhag was not seen in any patient. Sixty percent (n=35) patients were treated with phlebotomy, hydroxyurea and aspirin alone or in combination. None of the patients transformed to myelofibrosis (MF) ormyelodysplasia (MDS) during the mean (±SD) followupperiod of 57.2±50 months.One patient with ET transformed to acute myeloid leukaemia9 yearsafter the diagnosis. Conclusions: This study demonstrated a relatively more benign form of PV, ET and IMF with lesser frequency of symptoms, good response to treatment andless likelihood of transformation to MF, MDS or AM

Discrepancy between PCR based SARS-CoV-2 tests suggests the need to re-evaluate diagnostic assays

Objective: We investigated the discrepancy between clinical and PCR-based diagnosis of COVID-19. We compared results of ten patients with mild to severe COVID-19. Respiratory samples from all cases were tested on the Roche SARS-CoV-2 (Cobas) assay, Filmarray RP2.1 (bioMereiux) and TaqPath™ COVID19 (Thermofisher) PCR assays.Results: Laboratory records of ten patients with mild to severe COVID-19 were examined. Initially, respiratory samples from the patients were tested as negative on the SARS-CoV-2 Roche® assay. Further investigation using the BIOFIRE® Filmarray RP2.1 assay identified SARS-CoV-2 as the pathogen in all ten cases. To investigate possible discrepancies between PCR assays, additional testing was conducted using the TaqPath™ COVID19 PCR. Eight of ten samples were positive for SARS-CoV-2 on the TaqPath assay. Further, Spike gene target failures (SGTF) were identified in three of these eight cases. Discrepancy between the three PCR assays could be due to variation in PCR efficiencies of the amplification reactions or, variation at primer binding sites. Strains with SGTF indicate the presence of new SARS-CoV-2 variant strains. Regular modification of gene targets in diagnostic assays may be necessary to maintain robustness and accuracy of SARS-CoV-2 diagnostic assays to avoid reduced case detection, under-surveillance, and missed opportunities for control

Distribution of chromosomal abnormalities commonly observed in adult acute myeloid leukemia in Pakistan as predictors of prognosis

Objective: The heterogenous response to treatment in acute myeloid leukemia (AML) can be attributed largely to the difference in cytogenetic features identified in between cases. Cytogenetic analysis in acute leukemia is now routinely used to assist patient management, particularly in terms of diagnosis, disease monitoring, prognosis and risk stratification. Knowing about cytogenetic profile at the time of diagnosis is important in order to take critical decisions in management of these patients. The study was conducted to determine the distribution of cytogenetic abnormalities in Pakistani adult patients with AML in order to have insights regarding behavior of the. method: A retrospective analysis of all the cases of AML (≥15years old) diagnosed at Aga Khan University from January 2011 to December 2016 was performed. Cytogenetic analysis was made for all cases using the trypsin-Giemsa banding technique. Karyotypes were interpreted using the International System for Human Cytogenetic Nomenclature (ISCN) criteria. Result: A total of 321 patients were diagnosed with AML during the study period, of which 288 samples successfully yielded metaphase chromosomes. The male to female ratio was 1.7:1. A normal karyotype was present in 61% (n=176) of the cases whereas, 39% (n=112) had an abnormal karyotype. Of the abnormal cases, t (8;21) (q22;q22) and t (15;17) (q22;q12) were identified in 8.3% and 4.9% cases respectively. Adverse prognostic cytogenetic subgroups including complex karyotype, monosomy 7 and t(6;9)(p23;q34) were identified in 9%, 1% and 0.7% patients respectively. Conclusion: This largest cytogenetic data in adult AML from Pakistan showed comparable prevalence of favorable prognostic karyotype to international data. The prevalence of specific adverse prognostic karyotype was low