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Department of Molecular Genetics

Knowledge hub and pathology continuing medical education resource center.

Technology used

  • Next Generation DNA Sequencing (NGS)
  • Sanger’s DNA sequencing
  • Real-Time Polymerase Chain Reaction (RT-PCR)
  • End Point Polymerase Chain Reaction (PCR)
  • Karyotyping and Cytogenetic Analysis
  • Fluorescence In-situ Hybridization (FISH)

Dr. Saadat Ali

Head of Department (Consultant Molecular Geneticist)

Mphil, PhD in Biological Science, Certificate in DNA analysis (USA)

Quality Assurance

Daily monitoring of the internal QC program. Taking part in external QC programs such as College of American Pathologists Proficiency testing.

Next Generation Sequencing (NGS)

DNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA. It includes any method or technology that is used to determine the order of the four bases: adenine (A), guanine (G), cytosine (C), and thymine(T). The advent of rapid DNA sequencing methods has greatly accelerated biological research and medical diagnostics. Comparing healthy and mutated DNA sequences can diagnose different inherited and acquired diseases including various cancers, and can be used to guide patient treatment. Having a quick way to sequence DNA allows for faster and more individualized medical care to be administered.

Classical Sanger’s Sequencing can read a particular single short fragment of DNA and it is useful for single-gene disorders but has limitations in its application in complex multigenic inherited disorders and syndromes. In 2005, “next-generation sequencing”, commonly referred to as NGS, was introduced to sequence multiple target regions of DNA simultaneously after generating a library of the sequences of interest. The NGS technology follows the “sequencing by synthesis (SBS)” principle, based on a solid-phase method on a single substrate—resulting in a massively parallel and scalable method with unprecedented speed. The resulting output is millions of DNA sequence reads that can be used for downstream applications such as gene expression analysis, variant detection, or de novo genome assembly.

Next-Generation Sequencing system at Chughtai Lab is the latest technology based on standard sequencing chemistry, but with a novel, semiconductor-based detection system. Using this modern tool of biotechnology, disease-related gene-panels, or even a whole set of around 30,000 genes (Whole Exome) can be sequenced and analyzed for the detection of diagnostic or prognostic mutations that serve as disease biomarkers. BRCA1/BRCA2 gene panel for breast cancer, Pre-Natal Genetic Screening, Cancer Hotspot Panel are examples of testing services that can be provided using NGS.

Competitive Advantage of Molecular Genetics

The department of Molecular Genetics has recently been established at Chughtai Lab for the prenatal screening and molecular diagnosis of genetic disorders in children and adults.  This facility may also be used for screening of healthy individuals as well as for training and research.  We would be able to detect mutations including substitutions, deletion, insertions, and duplications in a single gene or selected panel of genes in including Oncological, Neurological, Hematological, and Metabolic disorders. 

The molecular genetics department will focus on the implementation of the latest molecular technologies for the following applications: 

  • Testing for Chromosomal Aberrations
  • Detection of pathogenic mutations in the single-gene disorders 
  • Prenatal screening and detection of disease-related mutations in targeted gene panels and across the entire genome using NGS

Current Parameters at Molecular Genetics Department include BCR-ABL Quantitative PCR Assay, HLA B-27 PCR, JAK-2V617F Mutation Detection, BRAF Mutation Analysis, KRAS Mutation Analysis, EGFR Mutation Analysis, BCR-ABL Fusion Detection by FISH, and Karyotyping and chromosomal analysis. In the future, we will keep on adding new molecular genetics assays to our list.