Showing posts with label Genomics. Show all posts
Showing posts with label Genomics. Show all posts

Friday, June 26, 2026

Pakistani-American Professor Publishes Landmark Genomic Research on Pakistanis

Dr. Danish Saleheen, a Pakistani-American professor at Columbia University, and his fellow researchers have published a comprehensive analysis of 173,303 genomes from Pakistan, one of the largest genomic studies ever conducted in South Asia. This landmark work is upending how scientists understand human genetics and drug development. "South Asians have been severely underrepresented in genome studies—comprising just 2% of global genomic databases despite representing 25% of the world's population," study leader Dr. Saleheen explained. The study is sponsored by Novartis, Columbia University Irving Medical Center, and the Center for Non-Communicable Diseases, Karachi, Pakistan. Its results could fundamentally transform drug discovery. 


The study, published in the journal Nature, has identified knockouts of nearly 6,500 genes—about one third of all protein-coding genes (exomes)—in 34,000 individuals. Cousin marriages are quite prevalent in Pakistan, with half of all marriages occurring between close relatives. Landmark research, including the Pakistan Genomic Resource, highlights how these genetic traits act as both a medical challenge and a massive opportunity for scientific discovery.  

Study of Knockout Genes in Humans vs Mice

What are "knockout genes"? In Pakistan, the study has identified thousands of individuals with naturally missing or "knocked out" or "deleted" genes. Researchers use mice for studying diseases and "knock out" or delete specific genes to study how the deletions impact health and contribute to disease. The problem is that translation of such findings to humans has been difficult, "because mouse genes often have different functions than their human counterparts," Saleheen says. “What’s unique about our Pakistan study is we can go back to participants and conduct comprehensive medical exams to see what kind of effects the gene deletion may have on the individual,” he adds.

The study reveals that South Asian populations carry genetic ancestry components shared with both European and African populations, suggesting that insights gained from the Pakistan Genome Resource (PGR) have broad applicability across multiple human populations. This genetic overlap means that treatments validated in Pakistani populations are likely to benefit diverse ancestry groups globally.

"What we would prefer to do is identify people who are born without working copies of these genes and see if that has an effect on their health."  These "human knockouts" are rare in genome databases like the UK Biobank and the NIH's All of Us, which predominantly contain genomes of people with European ancestry.  "Consequently, many experimental drugs that seem promising in mice fail in clinical trials," Saleheen says. "That costs billions of dollars in losses every year."

Dr. Saleheen is a physician-scientist working at the intersection of human genetics and drug discovery. He has an MBBS degree from Karachi's Aga Khan University and a Ph.D. in Cardiovascular Genomics from Cambridge University.  He is Professor of Medical Sciences and Director of Global Genomics at Columbia University Irving Medical Center, founding Director of the Center for Non-Communicable Diseases (CNCD) in Pakistan, and founding Principal Investigator of the Pakistan Genome Resource (PGR) — one of the world's largest human "knockout" discovery programs (www.cncd.org). He is the author of more than 250 research papers and a 2018 recipient of the Clinical Research Forum's Top 10 Clinical Research Achievement Award, the national prize recognizing the ten most outstanding clinical research accomplishments in the United States that year.

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Thursday, March 1, 2012

Genomics & Biotech Advances in Pakistan

Complete gene mapping of a Pakistani citizen by Human Genome Project in Karachi has put the country on a very short list of nations which have accomplished this scientific feat. To assess the state of genomics and biotechnology in Pakistan, let's take a look at what is happening in the country in this field:

1. Researchers at the Panjwani Center for Molecular Medicine and Drug Research (PCMD) in Karachi collaborated with Beijing Genomics Institute (BGI) to complete gene mapping of Dr. Ata-ur-Rahman, according to SciDev. Dr. Rehman, President of Pakistan Academy of Sciences, volunteered himself for the project.

2. More than two hundred life sciences departments are engaged in genomics and biotechnology research at various Pakistani universities, according to a report in The News.

3. Pakistan has been a Science Watch rising star for several years for research papers in multiple fields, particularly in biological sciences. Publications by Pakistani research teams have increased four-folds in the last decade, and the majority of publications from major universities are in life sciences.

4. Pakistan began producing biotechnology based pharmaceuticals in 2009. The first of these plants was set up by Ferozesons in Lahore to produce interferon for treatment of hepatitis, according to Nature magazine.

5. Pakistan has significant research efforts in seed and livestock development at various agriculture universities, institutes and departments. Pakistani researchers and scientists are currently collaborating in life sciences with their counterparts in the US and China. A number of crops like cotton, rice, wheat, corn, potato, ground nut are being developed locally or with the collaboration of Chinese and US seed companies.

6. Post-doctoral research on biotechnology and related agricultural issues is being funded under a Young Scientists Program, as part of the USDA-funded sustainable endowment to support the Agricultural Linkages Program at the Pakistan Agricultural Research Council (PARC). An MOU for $7.5 million has been signed under the Pakistan-U.S. Science and Technology Program between Pakistan’s Higher Education Commission (HEC) and the Ministry of Science and Technology and the U.S Agricultural Research Service (ARS) for scientific collaboration and capacity building of scientists.

7. National Biosafety Committee has allowed stacked gene (Cry 1A and Cry 2Ab) in cotton developed by Center of Excellence in Molecular Biology (CEMB), Lahore. Several other stacked gene products are in the pipe line and will be put for approval soon.

8. Pakistan is building the capacity of its young scientists in the legislative, regulatory, and policy areas related to agricultural biotechnology, biosafety and nanotechnology. A small project has been funded in Agricultural Nanobiotechnology related to the use of nanoparticles for plant genetic engineering utilizing a Bio-Rad biolistic gene gun at National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad.



While the universities have stepped up their research programs in life sciences as a result of the higher education reforms undertaken in the last decade, it's still a major challenge to translate the academic work into tangible benefits in terms of improved human health and higher crop and livestock yields in the country.

Part of the challenge stems from the need for regulatory framework for introducing biotech products and technology for humans, plants and animals. To make progress on this front, Pakistan has ratified the Cartagena Protocol of Biosafety (CPB) with a framework for handling GMO’s. The proposed regulatory guidelines are built upon on a three-tier system composed of the National Biosafety Committee (NBC); a Technical Advisory Committee (TAC); and Institutional Biosafety Committees (IBC), according to USADA GAIN report on Pakistan.

In the regulatory framework, the Secretary of the Ministry of Environment heads the NBC, and is responsible for oversight of all laboratory work and field trials, as well as authorizing the commercial release of GM products. The three monitoring and implementing bodies administer enforcement of the National Biosafety Guidelines. The IBC may make recommendations to the NBC regarding the awarding of exemptions for laboratory and fieldwork related to products of bioengineering. These recommendations may be accepted, and formal approval granted, if sufficient information and grounds exist to consider the risk as being minimal or non-existent. After permission for deregulation is granted by the NBC, approval can still be withdrawn provided sufficient technical data and other evidence later becomes available that warrants a review. The other important ministry dealing with production and release of GM crop is Ministry of Food and Agriculture (MINFA). The ministry developed several Standard Operating Procedures (SOP’s) for handling of cases of import/approval/release of GM crops; however, all these have yet to be promulgated.

Genomics and biotechnology have great potential to fight diseases and help improve human lives and increase productivity. So far, the benefits of these advances have accrued mostly to the rich countries because they are driven by market incentives. The time has now come for Pakistan to take advantage of such technological advances. Take crop yields as an example. Wheat is the staple of Pakistan and planted on the largest acreage. It contributes about three percent to the GDP. The national average yield is about 2.7 tons per hectare, far below the average in European countries such as France, Germany and the United Kingdom where they are above seven tons per hectare, according to recent Op Ed by Dr. Ata-ur-Rehman.

There is significant opposition to the use of GM seeds in South Asia today. In his book The Rational Optimist, author Matt Ridley recalls that there was similar resistance in 1960s to Nobel Laureate Norman Borlaug's Mexican dwarf wheat. Ridley writes about how Borlaug's efforts helped spark the Green Revolution in India and Pakistan. Ridley argues that it was Borlaug's work with his new seeds and chemical fertilizer that disproved Paul Ehrlich's claim in his book The Population Bomb that India would never feed itself.

Pakistani farmers have already begun planting biotech cotton since 2011. With 2.6 million hectares of Bt cotton planted in 2011, Pakistan ranks 8th in terms of the area for biotech crops in the world, according to International Service for the Acquisition of Agri-Biotech Applications (ISAAA) report. US ranks number 1, Brazil 2, Argentina 3, India 4, Canada 5, China 6, Paraguay 7 and Pakistan 8. South Africa 9 and Uruguay 10 round out the top 10. Pakistan has had a bumper crop of cotton in 2011-2012 mainly because of the planting of Bt seeds.



While extra caution is absolutely warranted before introducing genetically modified organisms in the environment, an irrational fear of the unknown would be unacceptable in a country like Pakistan with its dwindling water resources and a growing young population that needs to be fed, clothed, educated and nurtured. Clearly, the technology can help cure diseases and lead to development of new drought-resistant seed varieties producing high crop yields.

Related Links:

Haq's Musings

Pakistani Students Studying Abroad

Pakistan Manufacturing Tablet PCs

Military's Role in Pakistan's Industrialization

Pakistan's Demographic Dividend

Pakistan's Defense Industry Goes High-Tech

Pakistan Launches UAV Production Line at Kamra

Pakistan Going Mainstream in IT Products

Pakistan Launches 100 Mbps FTTH Access

Pakistan's $2.8 Billion IT Industry

Pakistan's Software Prodigy

Developing Pakistan's Intellectual Capital

Pakistan Graduation Rates Higher Than India's

Pakistan Conducting Research in Antarctica

Pakistani Scientists at CERN

Higher Education Reforms in Pakistan