Molecular Pathology


Presently, there is no structured residency program in the Section; however, residents from Histopathology, Microbiology, and Chemical Pathology and Hematology sections rotate in Molecular Pathology as a part of their comprehensive training program. Residents acquire special knowledge of molecular pathology on issues related to the application of DNA/RNA technology in wide variety of clinical circumstances. For example, in infectious diseases, they learn molecular diagnosis of several of the common viral and bacterial agents prevalent in Pakistan. Residents also learn how to correlate clinical findings and other laboratory tests with molecular diagnostic reports. Moreover, Molecular Pathology has recently, initiated a 2-year Fellowship program in which fellows learn about Molecular basis of disease and its latest diagnostic systems. In addition, through the Elective Rotation Program, AKU students and visiting medical students are taught the latest molecular techniques and their applications in infectious diseases cancer and genetic disorders. The Section also participates in the Technologist Training Program of the clinical laboratory Trainees are provided knowledge and skills of several molecular diagnostic techniques, results interpretation and different aspects of quality assurance.


The research activities of the Section include several areas of investigation. These activates are supported by both internal and external peer-reviewed grants received by the faculty.

One major theme of research is the study of Immunopathology of mycobacterial infections and the role of chemokine activation in the outcome of tuberculosis in pulmonary and extra-pulmonary infections. The intended goals of these projects are to understand the molecular and cellular basis of the difference between immune responses in localised and extrapulmonary tuberculosis. Another area of research interest of our faculty is to investigate molecular epidemiology of M. tuberculosis strains, to enhance our understanding of prevalence and transmission patterns of tuberculosis in Pakistan using spacer-oligotyping and IS6110 RFLP typing techniques.

The second area concerns identification of mutations in BRCA1 gene in breast cancer patients with family history. In our population, contribution of hereditary breast cancer equals to 15 to 20 per cent of the total cases. A plausible reason for this observation may be the fact that marriages within ethnic groups and especially between close relatives are very common in our population. Identification of BRCA1 mutations will help families' early detection of individuals at risk of breast cancer.​


The revolutionary advances made in molecular biology in the last few decades have made major impact on clinical laboratory diagnosis. This is evident from rapid acceptance and adoption of molecular diagnostics in laboratories around the world. Increasing awareness of molecular basis of disease and advancement in technology has increased the demand for nucleic based testing; molecular pathology offers novel strategies for gene therapy protocols, which have potential for use in future to correct genetic defects and treat cancer. Our team of qualified technical staff and consultants pay great attention to the development of high quality molecular tests.

Molecular Pathology Section was established in 1995 in Clinical Laboratories of the Aga Khan University Hospital. It performs nucleic acid based testing to provide diagnostic information to clinicians in order to help guide optimal care for patients with cancer, viral infection, histocompatibility and genetic diseases. Apart from performing complex Molecular testing support is also provided for research studies. A variety of both qualitative and quantitative virology tests based on viral nucleic acid detection using Real Time polymerase chain reaction for Hepatitis viruses (B, C and D types), Herpes Simplex virus 1&2, Cytomegalovirus, Dengue Virus, Epstein Barr virus and Cremeon Congo hemorrhagic fever virus represent the major viral types analyzed in the Molecular Pathology Laboratory. These tests help clinicians identify the correct diagnosis and monitoring of treatment. Molecular Pathology also offer Mycobacterium tuberculosis diagnostic test for detection of current and latent infection using PCR and IGRA technology.

DNA technology also provided powerful tools for genetic diagnosis, especially of single gene disorders such as thalassemia, cystic fibrosis, and others. Presently, the Molecular Pathology Laboratory offers prenatal diagnosis for ß-thalassemia, and, to date, more than 1000 tests have been successfully performed. In addition,F508 mutation screening, Spinal Muscular Atrophy, Duchene Muscular Atrophy,  interleukin 28B variant (rs12979860) analysis are also part of test menu. Human Leukocyte Antigen (HLA) matching is an important criterion for organ transplant. Molecular Pathology Laboratory provides low to intermediate resolution nucleic acid based typing facility for HLA class I and II loci. HLA-A, -B, -C, -DR, -DQ alleles are typed using PCR-SSP technology obtained from leading manufacturers. Mover Over HLA –B27 and HLA-B57 tests are also available for disease association. For post-transplant monitoring quantification of donor chimerism is also included in the repertoire

New innovations in genomic technologies in conjunction with advancements in biomarker discoveries have transformed approach towards cancer management. Molecular Pathology offer BCR-ABL1 translocations Qualitative and Quantitative analysis, BCR-ABL kinase Domain Mutation, PML RARA, FLT3 ITD and D835 and NPM, EGFR mutation analysis. . The vision of Molecular Pathology Laboratory is to make availab​le latest and high quality DNA diagnostics to improve health.​