What is Genomics?
Genomics aims to study the entirety of an organism’s genes. Beginning with the Sanger family of methods in 1977, there have been a major innovation in the field led by the induction of high-throughput deep or so-called next generation sequencing (NGS) technology.
Why a Genome Sequencing facility at PHRL?
The rise of highly contagious infectious diseases pose a significant threat to global health, including the potential of major pandemics. To effectively deal with this evolving threat, PHRL-KP, a leading COVID-19 testing lab felt the need of an in-house sequencing facility to reveal genomic diversity of emerging and remerging pathogens at much lower cost and with much greater precision.
The inception of Advanced Center for Genomic Technologies (ACGT) as part of the public health reference lab (PHRL), Khyber Medical University was supported by both national and international bodies including the WHO, NIH, and KP Health Department. The facility currently houses a portable single-molecule long-read sequencer from Oxford Nanopore for whole genome and a SeqStudioTM genetic analyzer from Thermo Fisher Scientific for targeted gene sequencing. Induction of a Miseq system from Illumina is in the pipeline.
What have we achieved?
ACGT has successfully optimized targeted and whole-genome sequencing of SARS-CoV-2. We have submitted a total of 120 partial and 30 whole-genome sequences of circulating SARS-CoV-2 strains to GISAID database.
What we do?
At present the lab focuses on genomics-based surveillance of SARS-CoV-2 using both 3rd generation Nanopore and Sanger Sequencing technologies. The goal is to track spread of SARS-CoV-2, find new variants and guide public health choices. With the currently underway transition, PHRL will be extending its services and will be able to test BSL-II plus level pathogens such as Congo fever, Dengue fever, Typhoid, and Cholera.
Workflow
Like all viruses, SARS-CoV-2 evolves over time through random mutations. Using these little changes, we can draw up phylogenetic trees, much like family trees. We can also make connections between different cases of COVID-19 and gauge whether there might be undetected spread of the virus.
Our Vision
The Genomics Center aims to be the national leader in genomic medicine research offering high-end genomic solutions to researchers working in the fields of microbiology, infectious diseases, cancer biology and human molecular biology. A key component of this transition will be recruiting and retaining personnel with the specialized skills and experience who will train subspecialists in their respective areas to competently address provincial and national healthcare needs.
Our Team:
Dr. Yasar Mahmood Yousafzai (Assoc. Prof & Director PHRL)
Dr. Ishaq N Khan (Assist. Prof. in-charge)
Mr. Muhammad Zakria (Scientific Officer & Team lead)
Dr. Muhammad Iqbal Qureshi (Virologist, Bioinformatician)
Mr. Tariq Rahim (Molecular Biologist)
Dr. Waseem Shah (Molecular Biologist)
Mr. Shahzad Ahmad (Lab Technologist)
Mr. Hanif Ullah Khan (Lab Technologist)
