Day 1 :
Keynote Forum
Petr Starostik
University of Florida in Gainesville, FL
Keynote: Implementation of NGS Causes Dynamic Shifts in Clinical Molecular Diagnostics
Time : 09.30-10.00
Biography:
Dr. Petr Starostik is Associate Professor of Pathology and serves as Director of Molecular Pathology in the Department of Pathology, Immunology, and Laboratory Medicine of the College of Medicine at the University of Florida in Gainesville, FL. Over the years, he directed several molecular diagnostics laboratories, both in the U.S. and abroad. Development of molecular diagnostic tests is his specialty as evidenced by his publications and the multitude of laboratory-developed tests performed in laboratories he directed. Besides clinical work, he also pursues basic research focusing on the role of FLT3 ITD in acute leukemia.
Abstract:
The past decade witnessed a truly revolutionary change in ways how mutation detection is performed in a clinical laboratory. Single analyte tests were replaced in many labs by multianalyte next-generation sequencing, NGS. This technique significantly decreased sequencing cost pre base, enabled labs to analyze much higher number of samples at once, and broadened the analysis scope from a single gene to gene panels or even the whole exome/genome. Many new so far unknown gene mutations were discovered by NGS. They can be used as biomarkers in diagnosis and their availability led to changes in tumor classification. They are also potential drug targets to develop targeted therapies for. Several manufactures supply NGS instruments and reagents to detect both somatic and germline mutations. Many laboratories opt to develop their own laboratory-developed NGS assays which can be easily tailored to meet their needs. We developed both amplicon- and hybridization probe-based NGS assays used to detect driver and druggable mutations in different types of cancer. The assays were extensively validated and allow for quick and sensitive detection of point mutations and indels for the most relevant therapeutic genes in several types of cancer. The complexity of NGS does not make its implementation easy. NGS wet lab workflow entails several critical steps like sample and sequencing library preparation which are critical for success. Bioinformatics is an integral part of NGS and needs to be handled by an experienced IT specialist to not only develop he appropriate analysis pipeline but to also make the results available in the appropriate format in the electronic medical records. Administrative leadership is needed to secure proper reimbursement and keep track of government regulations and oversight.
Keynote Forum
Hong L Drum
Genoptix Medical Laboratory, USA
Keynote: Chronic myelogenous leukemia with B-lymphoid blasts crisis at presentation: A case report and literature review
Time : 10:30-11:00
Biography:
Hong L Drum has completed her MD from Guangdong Medical University, China. Dr. Hong L. Drum is a senior Hematopathologist at Genoptix Medical Laboratory, a Novartis company.
Abstract:
Chronic myelogenous leukemia (CML) with B-lymphoid blast crisis at presentation is rare. We present a case of a 52-year-old female without a prior known history of hematologic malignancy, who presented with CML with B-lymphoid blast crisis. Review of peripheral blood smears showed moderately increased white blood cells with left-shifted granulocytosis and basophilia. Bone marrow core biopsy demonstrated markedly increased cellularity with marked, left-shifted myeloid hyperplasia. Megakaryocytes were increased with frequent small hypolobated forms. Blasts were increased, comprising 22% of the marrow. The blasts were positive for PAX-5, CD10, CD19, CD34, and TdT, and negative for MPO, consistent with B-lymphoblasts. Quantitative PCR detected BCR-ABL1 transcript (the major breakpoint, p210) at 70.5820% on the International Scale. T(9;22)(q34;q11.2) was detected by cytogenetic study. A diagnosis of CML with B-lymphoid blast crisis at presentation was rendered based on the above findings. Distinguishing a CML with B-lymphoid blast crisis at presentation from a de novo B-acute lymphoblastic leukemia (B-ALL) with t(9;22) often is not easy. The morphologic features that point to a CML with B-lymphoid blast crisis rather than a de novo B-ALL with t(9;22) include concurrent presence of basophilia and left-shifted granulocytosis in the blood, and left-shifted myeloid hyperplasia and increased small atypical megakaryocytes in the bone marrow. Among these morphologic features, the presence of small atypical megakaryocytes/micromegakaryocytes in the bone marrow is considered to be most specific, although not all CML in B-lymphoid blast crises have this morphologic feature.
Keynote Forum
Cynthia Lorenzo
Genoptix Medical Laboratory, USA
Keynote: Refractory anemia with ring sideroblasts, with JAK2 and SF3B1 mutations, without thrombocytosis: a case report and review of literature
Time : 11:50-12:20
Biography:
Dr. Cynthia Lorenzo completed her M.D. at 29 years of age from Stanford University School of Medicine. Dr. Lorenzo is a senior Hematopathologist at Genoptix Medical Laboratory.
Abstract:
JAK2 mutations are rare in refractory anemia with ring sideroblasts (RARS). We present the case of an 83-year-old female who presented with anemia and no evidence of cytosis. Blood count revealed the following: WBC 4.9 K/uL, Hgb 9.7 g/dL and platelets 174 K/uL. The marrow was variably cellular and showed trilineage hematopoiesis. Erythroid precursors appeared normal in number; however, numerous ring sideroblasts were identified. There were no karyotypic or FISH abnormalities. Molecular studies using next generation sequencing technology showed both JAK2 and SF3B1 mutations. These findings were most consistent with a myelodysplastic syndrome, RARS. SF3B1 mutations are associated with a favorable prognosis in MDS, and are highly predictive for the presence of ring sideroblasts. The presence of the JAK2 mutation in this patient is unusual. JAK2 mutation usually leads to cytokine hypersensitivity and cytokine-independent growth of hematopoietic cells resulting in uncontrolled proliferation and a myeloproliferative phenotype. JAK2 mutation is rare in myelodysplastic syndromes such as RARS. However, the presence of both JAK2 and SF3B1 mutations has been seen in cases of myelodysplastic/myeloproliferative neoplasms (MDS/MPN), such as RARS associated with marked thrombocytosis (RARS-T). The current case had normal platelet count, and therefore did not satisfy the criteria for RARS-T. The possibility that this patient would later develop an MDS/MPN cannot be excluded. The reason that some MDS patients with JAK2 mutation do not develop a myeloproliferative component is unknown. Further studies are needed to determine the role of JAK2 mutation in these MDS patients.
- Clinical Applications of Molecular Biology | Cytogenetics | Clinical Coagulation | Molecular Pathology | Blood transfusion | Laboratory Management | Clinical Microbiology | Urinalysis & Diagnosis | Medical Microscopy | Laboratory Toxicology
Chair
Petr Starostik
University of Florida, USA
Co-Chair
Sarah Adelaide Crawford
Southern Connecticut State University, USA
Session Introduction
Parviz Parvizi
Pasteur Institute of Iran
Title: Evaluating and Setting up a qPCR by High Resolution Melting method for definitely discrimination of Leishmania species by targeting amino acid permease 3 gene
Biography:
Parviz Parvizi has completed his PhD from the London School of Hygiene and Tropical Medicine (London University) and Natural History Museum (London) in 2004. He has been a Full Professor from 2015 and has been appointed as the Head of Parasitology department and also as the Director of Parasitology, Immunology and Mycology Research Group at Pasteur Institute of Iran. He has published more than 60 papers in reputed journals.
Abstract:
Leishmania as protozoan parasites causes major diseases of leishmaniasis in humans in tropical and subtropical regions. In different hosts including humans, clinical samples, rodents and/or other mammals as reservoir hosts and sand flies as vectors, mixed infections, co-infections and different hybrids of Leishmania parasite with different aneuploidy in chromosomes are observed. Differentiate common Old World parasite species and discriminate co-infection with different species. The genetic variation analysis and SNP prediction identify using high resolution melting analysis as a powerful method. For each species, one standard sample was amplified and a recognized region was cloned. Three sets of primer were designed for nuclear gene of amino acid permeases (AAP3) gene and EvaGreen dye mechanism was used and the different temperature of HRM species was optimized. Temperature variation in HRM separated L. major and L. tropica co-infections and their sub-strains. The specific and common primers were separate species and strains by melting temperature analysis. To compare with variety of mitochondrial and nuclear genes, AAP3 gene is more sensitive and specific than other genes for identification of Leishmania parasites. The setup HRM could separate common species of Leishmania parasite and useful in separations intra-stains. Efficiency and regression coefficient reactions for genus and species Leishmania were also validated.
Jyotsna Agarwal
King George’s Medical University
Title: Comparative gene expression of urine and fecal E. coli isolated from women with acute cystitis
Biography:
Jyotsna Agarwal has joined at the King George’s Medical University, Lucknow as a Faculty in 2002 and is currently working as a Professor of Microbiology, In-charge Bacteriology Laboratory. She received her MBBS degree from CMC, Vellore and MD in Microbiology from BHU, Varanasi. She is Nodal Officer In-charge for Regional Centre of WHO sponsored Diphtheria Surveillance Project and Regional RTI/STI Centre for state of Uttar Pradesh. Her research interests include antimicrobial resistance, molecular diagnostics; focus areas are infections of children including pneumonia, septicemia and meningitis; sexually transmitted/reproductive tract infection along with pathogenesis of urinary tract infections in women. She has nearly 50 publications in reputed journals and a book chapter to her credit.
Abstract:
Temporal and spatial regulation of gene expression induced by bladder environment may be accountable for difference in the pathogenicity of urinary and fecal E. coli isolates. In order to better understand the pathogenesis of urinary tract infection (UTI), genetic and functional (expression) profiles of cystitis and fecal E. coli isolates were analyzed in present study. Fifty sets of concurrent urinary and dominant fecal E. coli from women with acute cystitis were correlated by analyzing their mRNA and phenotypic expression for five virulence genes (VGs) viz. fimH, papG alleles, hlyA, iutA and traT along with phylogenetic grouping. Predominance of phylogenetic group B2 (48% and 40%, respectively) and higher prevalence of VGs fimH (82% and 78%), followed by traT (66% and 46%), and iutA (44% and 40%) was observed in both urinary and fecal E. coli isolates, respectively; with traT being the only gene significantly associated with urinary isolates (p=0.04). Number of urinary E. coli expressing mRNA and corresponding phenotype of the respective gene tested was more in urinary isolates as compared to fecal isolates; though this difference was statistically significant only for traT (p=0.02). Differences between genetic and expression profiles of concurrent dominant fecal and cystitis E. coli were not prominent; indicating establishment of symptomatic infection might be more dependent on the host factors rather than on the virulence potential of uropathogens alone.
Moonira Mullah
Cape Peninsula University of Technology
Title: Global Perceptions of the Profession of Medical Laboratory Sciences
Biography:
Abstract:
Biomedical Laboratory Technologists or Scientists play a fundamental role in diagnosis and disease management of patients. “South Africa has the largest economy in Africa but is one of the most inequitable societies in the world, illustrated by the disparity between private and public sector healthcare funding. Eighty-four percent (84%) of South Africans cannot afford to contribute to private health care insurance and are thus reliant on the public health care systems which utilise the laboratory services provided by the National Health Laboratory Services (NHLS). The NHLS provides South Africans access to pathology services in both the private and state funded medical laboratories. The service provides a comprehensive range of laboratory tests across all Medical Laboratory Science disciplines. A mere 16% of the South African population belong to private medical aids which gives them greater benefits for utilisation of private pathology laboratory services after consultation with a clinician. These private pathology laboratories provide additional comprehensive specialised diagnostic analyses for patient treatment.
This was a qualitative study making use of semi-structured open ended questions. Over 480 surveys were sent out using an online programme called Survey Monkey. There was a response rate of 32.4%.
Majority of the respondents were Medical Technologist employed in private pathology laboratories. Approximately 98.59% of respondents were registered with the Health Professions Council of South Africa, however, only 54.23% were active members of the Society of Medical Laboratory Technologist of South Africa. The majority of respondents were female with job satisfaction of approximately 71.90%. More than 30% of respondents were employed for longer than 15 years with their current employer
Asma Shabbir Hussaini
Jinnah Sindh Medical University
Title: Evaluation of Human Epidermal Growth Factor Receptor (Her-2/neu) in Gastric Adenocarcinoma: A Study from South Asia region
Biography:
Dr. Asma Shabbir has done MBBS from B.J.M.C, Pune University, India. She has done her post-graduation from Dow International Medical College & University, Karachi, Pakistan. She is a gold medalist throughout her career. She has a passion towards research & concerned for better prognosis of the patient. She has presented her research work in many conferences. Recently she received "Young Researcher Award" in International Conference of Digestive Diseases held in Dubai 2016. She has also reviewed articles from International Journals. She is a member of different scientific & research associations. At present she is working as researcher & Assistant Professor in Department of Pathology, Jinnah Sindh Medical University, Karachi, Pakistan.
Abstract:
Background & Aim: Gastric cancer is the third leading cause of cancer mortality worldwide. Human epidermal growth factor (Her-2/neu) has shown strong therapeutic implication in breast cancer. Expression of Her-2/neu in gastric cancer has been reported from across the world, it is still unknown from South Asia region. The aim of this study is to evaluate Her-2/neu expression in gastric adenocarcinomas and to correlate with various clinico-pathological variables.
Patients & Method: A total of 95 consecutive patients undergoing endoscopic biopsy or gastrectomy were recruited in this study after institutional ethical approval. Clinico-pathological parameters of all patients were recorded and hematoxylin and eosin (H&E) staining was performed. Expression of Her-2/neu was investigated by immunohistochemistry using a-Her-2 antibody. Hofmann validation scoring system was used and its association was seen with various clinicopathological variables including age, gender, histopathological type, grade and stage of the tumor.
Results: Her-2/neu over expression was found in 21 (22.1%) cases from the total of 95 gastric adenocarcinomas. Her-2/neu was significantly expressed in low grade gastric cancer (p=0.030). Although there was no significant difference between Her-2/neu expression and other variables, Her-2/neu score 3+ was higher in females, age >60 years, Laurens intestinal type and IIIC stage.
Conclusion: Her-2/neu is expressed in a limited group of gastric cancer patients in Pakistani population. Our findings indicate a significant strong association of Her-2/neu expression with low grades of gastric cancer.
Eric S Donkor
University of Ghana
Title: A genomic infection control study for Staphylococcus aureus in two Ghanaian hospitals
Biography:
Eric S Donkor has done his Doctoral degrees in Infectious Diseases and Public Health from London School of Hygiene and Tropical Medicine, and University of Iceland, respectively. He holds Master degrees in Molecular Biology and Animal Microbiology from Birkbeck College, University of London and University of Ghana, respectively. He has received several researches funding and has published 50 peer reviewed articles in the areas of Infectious Diseases, Food Safety and Environmental Health. Currently, he is an Associate Professor of Public Health Microbiology at University of Ghana.
Abstract:
Staphylococcus aureus is a notorious hospital acquired pathogen and is implicated in several serious infections such as meningitis, bacteremia and pneumonia. Whole genome sequencing analysis (WGSA) provides the best resolution for typing of bacterial isolates and has the potential for identification of transmission pathways. We used WGSA to study isolates of S. aureus from the pediatric emergency ward of Korle-Bu Teaching Hospital (KBTH) in Ghana where a suspected outbreak had recently occurred. The dominant clone of S. aureus identified among the isolates was sequence (ST) 15. The genomics data indicated cross contamination of multiple surfaces in the emergency ward by multiple lineages of ST 15 with the door handle of the ward implicated as a potential transmission route. The data also suggests that ST 15 is widely disseminated at KBTH, as it was found in multiple infections in the hospital (during the period of the outbreak) that were unrelated to the transmission events in the pediatric emergency ward. This investigation highlights the need for proper disinfection of environmental surfaces at KBTH.