Oral Cancer Genomics Project

The Oral Cancer Genomics Project is an exploratory, data-driven pilot study that utilizes next-generation DNA sequencing technology to examine the molecular signatures of oral cancer in the local population in Pakistan. This means tumors from each patient in the cohort will be diagnosed in a more detailed manner by ‘reading out’ their total DNA alongside routine biopsy examination.

The study is led by the Precision Medicine Lab which is a joint initiative of CECOS University and Rehman Medical Institute and is funded by the Planning Commission at the Federal Government of Pakistan. The study has been granted IRB approval by the Research Ethics Committee at Rehman Medical Institute (Ref. No. RMI/RMI-REC/Approval/77 on December 07, 2020).

Key Investigators

Dr Faisal Khan
Dr Faisal Khan
Assistant Professor, CECOS University.
Dr Johar Ali
Dr Johar Ali
Head of Genomic Sciences, Rehman Medical Institute
Dr Zubair Durrani
Dr Zubair Durrani
Head of Oral and Maxillofacial Surgery, Rehman College of Dentistry

Purpose of the Study

  • Cancer is known to be a disease of accumulating mutations or errors in the DNA. These mutations or ‘errors’ can be inherited from parents in certain families and can also happen because of a person’s lifestyle and his or her environment.
  • Oral cancer or OSCC (Oral Squamous Cell Carcinoma) is a type of cancer which can develop in any of the part of the oral cavity (mouth) such as tongue, lips, cheeks, throat, soft and hard palate, and sinuses. The risk factors include alcohol, smoked tobacco (cigarette and cigars), smokeless tobacco and betel quid, poor oral hygiene and even a broken tooth.
  • In Pakistan, smokeless tobacco (naswar), areca nut (gutka), betal leaf (paan) and naswar, and alcohol is commonly used along with wide occurrence of poor oral hygiene practices. According to the World Health Organization, oral cancer is the second most prevalent and leading cause of cancer death in Pakistan after Breast Cancer, with an estimated 5-year prevalence of 36,560 cases, 18,881 newly diagnosed cases and 13,351 deaths in 2018.
  • Oral Cancer is poorly represented in most large scale international studies. One potential reason is the poor incidence of oral cancer in countries where this study is undertaken. Pakistan, on the other hand, also lacks data describing the characterization of oral cancer mutational spectrum (types and number of ‘errors’) in the local population, which is the main motivation of this study.

Information for Patients

  1. We will be enrolling patient volunteers after an informed consent process, during which all details of the study and any associated risks will be laid out to the patients and their families.
  2. Due to the nature of the study we will only be enrolling recently diagnosed patients who have not undergone any therapy or surgery yet. Biopsy-confirmed, OSCC patients of all ages and all genders will be recruited in the study who are awaiting their surgery.
  3. After informed consent, we will get relevant details about the patient including laboratory tests and patient history and also a blood and saliva sample a day before the patient’s surgery. We will then coordinate and collect a tumor sample from the surgery team on the day of the surgery. All samples are collected under strictly-followed protocols and are delivered to the Lab through a fully documented process.
  4. Upon arrival to the Lab, parts of the samples are used to extract total DNA to read the DNA sequence (whole exome analysis) and the remaining parts are used to generate primary cell lines that is used for drug screening. All samples and details are anonymized and kept safe under the 7-layers protocol.
  5. Any actionable information that comes out of these two types of experiments that can be useful for the patient is immediately passed on to the doctor concerned without any delays. Results of the entire projects are then published and shared publicly with the scientific community to benefit from and allow science and biomedical research to progress.

Information for Clinicians

  1. We are welcome oral and maxillo-facial surgeons and their teams of TMOs who treat oral cancer patients to join the study. After due process, the consultant is enlisted as a co-investigator and the relevant hospital is enlisted as a study site.
  2. Please get in touch with the Principal Investigator or the Study Coordinators to request an Onboarding Pack which has all the details and paperwork that can be sent to you by post.

Contact Details

Dr. Faisal Khan

Principal Investigator

Precision Medicine Lab


+92-91-5838000 Ext. 5234

Hina Zamir

OSGS Study Coordinator

Precision Medicine Lab