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FROM RESEARCH TO INDUSTRY: MOLECULAR DIAGNOSTICS IN SRI LANKA

FROM RESEARCH TO INDUSTRY: MOLECULAR DIAGNOSTICS IN SRI LANKA. MAYA B. GUNASEKERA, PH.D. GENETECH MOLECULAR DIAGNOSTICS & SCHOOL OF GENE TECHNOLOGY , COLOMBO 8. Background of Research ….

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FROM RESEARCH TO INDUSTRY: MOLECULAR DIAGNOSTICS IN SRI LANKA

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  1. FROM RESEARCH TO INDUSTRY: MOLECULAR DIAGNOSTICS IN SRI LANKA MAYA B. GUNASEKERA, PH.D. GENETECH MOLECULAR DIAGNOSTICS & SCHOOL OF GENE TECHNOLOGY , COLOMBO 8

  2. Background of Research … Research in Molecular Biology – Initiated at Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Colombo 1991 First Ph.D. project - funded by NSF and TWAS, Italy. Biotechnology Laboratory, Faculty of Science, University of Colombo established in 1993 -through JICA grant. 3 Ph.D. projects initiated - One funded by IFS Sweden (1995) and two funded by the NSF (1996 and 1997). IAEA funded collaborative project initiated (1999) Total research funds received through these projects (1991-2000) - USD 70,000

  3. Research Output Number of Ph.D. thesis – 4 Development of DNA probes for An. culicifacies complex, Population genetic study of the Asian elephant in Sri Lanka, Development of DNA markers for the identification of humans in Sri Lanka - this project led to the use of DNA typing for casework in Sri Lanka Molecular systematics of a fruit bat species complex IAEA project on dengue led to the establishment of a molecular diagnostic assay for dengue in Sri Lanka Awards – TWAS/NSF Young Scientist Award, IFS, Sweden Jubilee Award, Post graduate Research Publication Award, President’s Research Award, University of Colombo Award for Excellence in Research , NSF Merit Award, Second best paper in an International Conference.

  4. Genetech – the first private biotech institute… • Inauguration was held in 2003 • Scientists 3 Post doctoral (one visiting) 1 M.D. , M.Sc. 1 M.Sc. 5 B.Sc. graduates • Total no. of employees – 16 Our mission – Is to make the benefits of biotechnology accessible to wider public in Sri Lanka

  5. Genetech Services • Molecular diagnostic services for infectious • and genetic diseases. • DNA profiling services to the public, including • civil and criminal casework • GM food testing - latest addition • Training courses in gene technology to • disseminate knowledge / to develop skills • related to biotechnology field

  6. Laboratory Diagnosis of disease – Traditional methods • Culture and Microscopy – morphological characteristics • Analysis of host and pathogen enzymes • Immunochemical tests (IFAT, HI, and ELISA) • Analysis of antibodies – indirect test • Analysis of antigens of pathogens –direct test All these methods are based on the detection of gene products.

  7. Nucleic acid-based diagnostics • All biochemical and physical differences can be traced back to differences in the genetic material. • Universal chemical and universal methods. • Detects the organisms rather than gene products of organism and host antibodies • Higher sensitivity – minute number of organisms present in a clinical sample can be detected due to the ability to amplify the DNA (by Polymerase Chain Reaction- PCR) found in a specimen. • Higher specificity and accuracy. • High throughput- large number of samples can be processed together. • Rapid screening of one sample for several organisms.

  8. Diagnosis of Infectious Diseases • Each organism has unique DNA regions - such regions have been cloned and DNA sequenced. • Primers have been designed to specifically amplify such regions by PCR if the organism is present in a clinical specimen. A million of copies of a DNA region unique to the pathogen PCR Product

  9. Detection of TB M S1 S2 S3 S4 WE DW +Ve 123 bp target product

  10. Progress in TB testing 2003-2005

  11. Some of the other bacterial tests offered …. Chlamydia Staphylococcus M S N M S1 S2 P N

  12. Testing for parasites… Malaria Filariasis W. bancrofti Plasmodium P.vivax P.falci

  13. Testing for DNA viruses …Herpes simplex Varizella Zoster PCR1 PCR2 M S1 N S1 N P M S1 S2 P N M S1 S2 P N

  14. Detection of Cytomegalovirus (CMV) and monitoring of drug therapy M S1 S2 S3 S4 S5 N After therapy Before therapy • Monitoring of antiviral therapy

  15. CMV testing-progress

  16. RNA viruses…. ‘SARS’- Corona virus Hepatitis C M S1S2 N N P M S1 S2 S3 N M S1 S2 S3 N 216 bp 110 bp

  17. Enterovirus group

  18. Dengue can be detected on first day of fever Detection of dengue D4 D2 D3 D1 Flavi DEN

  19. Dengue testing – seasonal trend

  20. More than 30 diagnostic tests have been established at Genetech….

  21. Latest additions….

  22. Testing for genetic disorders ….Duchenne Muscular Dystrophy S1 S2 S3 S4 S5 N M S1S2 S3 S4 S5

  23. Beta-thalassemia gene mutations M HbEN HbEM IVS1-5N IVS1-5M IVS1-1N I VS1-1M

  24. Leukaemia Screening –Philadelphia chromosome N P1 P2 S1 S2 S3 S4 M S5 S6 S7 S8 S9

  25. Genetic disorders tested…….

  26. DNA typing services… Rape/ sexual abuse Murder Child Abuse Incest Theft Positive identification of criminals Exoneration of innocent suspects Child maintenanc Custody Adultery Inheritance Immigration Establishment of paternity/family relationships Mutilated/decomposed bodies Establishment of identity

  27. DNA profiles generated by PCR typing STR locus

  28. DNA typing - progress

  29. No. of Parentage tests/District District

  30. Limitations of DNA-based diagnostics • Need special equipment, expensive chemicals and highly skilled staff • Accuracy and reproducibility depends on the technical experience of the operator • False negatives may arise due to PCR inhibition and false positives may arise due to PCR contamination. Therefore stringent quality control measures must be taken by the PCR Laboratory.

  31. Genetech services –Quality guaranteed…. • In-house PCR-based kits prepared based on published protocols • Validated with commercial kits/ with positive clinical specimens with each newly prepared reagents • All steps are subjected to well documented quality control and quality assurance procedures • All tests performed by trained, qualified staff • Pre & Post PCR physically separated • Use of Filter tips, separate pipettes and PCR hoods, negative controls with each assay – no short-cuts • Cheapest in the world.

  32. Genetech Training Courses…. • Training under the Ministry of Science & Technology Personnel Development project sponsored by ADB –18 personnel from the university sector. • Other Genetech courses – 184 persons trained • School children and undergraduates -lectures and demonstrations – > 1000 • In-house Training of Police Officers in handling and collection of DNA evidence – 205 • 4 hr training scheme for more than 2000 Police Officers

  33. Success cannot be achieved alone!!

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