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—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.  

What are "knockout genes"? In Pakistan, the study has identified thousands of individuals with naturally "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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Comment by Riaz Haq 1 hour ago

Zehra Farooq
@ZehraFarooq
On January 20, 2022, Pakistan's GDP grew by Rs 8.1 trillion overnight. Not a single factory opened. Not a single additional tax was collected. Public debt, frozen at Rs 39.9 trillion, did not change by a single rupee. But the debt-to-GDP ratio fell from 83.5% to 71.8%, instantly.

This is a thread about the institution behind that number, and why it urgently needs to be better funded

https://x.com/ZehraFarooq/status/2070915475232702960?s=20

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Zehra Farooq
@ZehraFarooq
The Pakistan Bureau of Statistics is the most consequential institution most Pakistanis never think about. It computes GDP, tracks inflation, counts us in the census, and tells us how many people are poor, what they earn, and how they spend.

Every IMF negotiation, every monetary policy decision, and every poverty programme in this country is built on PBS data. When the numbers are imprecise, so is the policy that follows from them.

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Zehra Farooq
@ZehraFarooq
This thread is built on seven consecutive years of official budget documents, Demands for Grants Vol. III, from FY2018-19 through FY2026-27, extracted line by line across all 35 PBS offices nationwide. The pattern you are about to see is not the story of a bad year or two. It is structural.

--------------------------


Zehra Farooq
@ZehraFarooq
Nine panels of seven years of data tell a consistent story. Total expenditure has grown from Rs 1.4 billion in FY19 to Rs 5.1 billion in FY27, which sounds like progress until you see that 71 paisa of every rupee still goes to salaries.

In FY23 that figure hit 91%, leaving nine paisa for everything else, travel, equipment, occupancy, and all operations combined. Travel as a share of the employee budget has never exceeded 14% in any year across this entire dataset. In FY23 it fell to 1.9%.

The institution doubled in nominal budget and remained structurally unable to sustain the fieldwork its mandate requires.

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Zehra Farooq
@ZehraFarooq
Budget 2026-27 allocates PBS a total of Rs 5.41 billion to run 35 offices and maintain 3,364 sanctioned posts. Of that, Rs 3.62 billion, 71%, goes to salaries and allowances before a single enumerator steps into the field.

The travel and transport budget, which funds all field data collection across the entire country, stands at Rs 298 million. The computer equipment maintenance budget is Rs 12 million. The capital investment budget for new equipment is zero.

PBS runs CPI from 35 cities, SPI from 17 cities every week, a quarterly Labour Force Survey, national accounts, and multiple sectoral data exercises on these allocations. This is a payroll that has been structured to look like a statistical agency.

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Zehra Farooq
@ZehraFarooq
Going back to January 20, 2022 when Pakistan rebased its national accounts, updating the reference year from 2005-06 to 2015-16.

Note that rebasing is standard and necessary practice, the IMF recommends doing it every five years, and Pakistan's base year was long overdue for an update.
The mechanics are straightforward: rebasing recalculates the economy's structure using more recent prices and broader sectoral coverage. The problem is that Pakistan lacked the underlying surveys to do it rigorously. There was no new livestock census, and no establishment survey adequately covering the informal sector.

The result was that GDP for FY2020-21 jumped from Rs 47.4 trillion to Rs 55.5 trillion overnight, the debt-to-GDP ratio fell from 83.5% to 71.8% without a single rupee of debt being repaid, the FBR tax-to-GDP ratio worsened from 9.6% to 8.5% because the denominator grew, and the FY21 growth rate was revised upward from 3.9% to 5.37%.

Nothing changed in the economy except for the measurement.

Comment by Riaz Haq 1 hour ago

Zehra Farooq
@ZehraFarooq
Had Pakistan never rebased in 2022, GDP in FY26 would read roughly Rs 108 trillion on the old methodology.

The official figure is Rs 126.9 trillion. That Rs 18.5 trillion gap is not real economic output, it is methodological uplift, and once embedded in the denominator, it automatically improves every ratio a government cares about. The sitting government at the time revised the FY21 growth rate from 3.9% to 5.37% overnight. Political fortunes and statistical choices were, as ever, deeply entangled.

https://x.com/ZehraFarooq/status/2070916736598303173?s=20

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Zehra Farooq
@ZehraFarooq
Legitimate concerns were raised about the quality of the 2022 rebasing. The livestock sector increased 18% at the base year without a livestock census to justify it. The construction sector was likely overstated by over 30% relative to available cement output data. The electricity sector showed a 75% jump in value added despite a circular debt crisis that implies distribution losses, not gains.

To be clear, I am not making an argument against rebasing — it is an argument for doing it properly, which requires better underlying surveys, which requires investing in
@PBSofficialpak

--------------------


Zehra Farooq
@ZehraFarooq
An here is more evidence of why: in FY2022-23, Pakistan's CPI averaged 29.2%, the highest since the 1970s. The State Bank used that number to set interest rates, the government used it for wage indexation, and the IMF used it for programme conditionality. In that same year, PBS had Rs 43 million to fund all field travel across all 35 offices for every survey it runs.

A back-of-envelope calculation makes the problem concrete: CPI collection across 35 cities, done to minimum international standards, requires roughly Rs 80 to 100 million in annual transport costs alone. Add the weekly SPI across 17 cities and the quarterly Labour Force Survey, and you are well past Rs 200 million before anything else is funded.

At Rs 43 million, the numbers do not add up. Something was cut, and the quality of Pakistan's most cited economic indicators in its worst inflation year in a generation was the consequence.

---------------



Zehra Farooq
@ZehraFarooq
There is more: the HIES — the Household Integrated Economic Survey, which is Pakistan's only reliable source of poverty measurement, consumption data, and income distribution, was not fielded for six years.

It was last conducted in 2018-19 and completed again only in 2024-25.

Those six years encompassed the COVID income collapse, catastrophic floods, 29% inflation, a near-default, and the largest real wage contraction in a generation. Pakistan has no direct distributional evidence of any of it. The CPI basket still reflects 2015-16 consumption patterns. The World Bank estimated that roughly 9 million Pakistanis fell below the poverty line in 2022 alone.

Pakistan had no domestic survey data to verify, challenge, or refine that number.

Comment by Riaz Haq 1 hour ago

Zehra Farooq
@ZehraFarooq
Budget 2026-27 allocates PBS Rs 5.41 billion to measure and report the statistics of a Rs 126.9 trillion economy. That is less than 0.004% of the GDP it is responsible for measuring.

India's NSO operates at roughly ten times Pakistan's relative statistical spend as a share of GDP. Even Bangladesh's statistical bureau receives comparable proportional funding.

Pakistan is asking its statistical agency
@PBSofficialpak
to run a 240-million-person economy's data infrastructure on the annual budget of a mid-sized university department, and then making consequential decisions about taxation, energy pricing, and social protection based on what that agency is able to produce.

https://x.com/ZehraFarooq/status/2070917509218554201?s=20

------------

Zehra Farooq
@ZehraFarooq
The ask is not complicated.

Field the HIES on its original biennial cycle and protect that budget line from being crowded out when the next census comes. Increase operational and transport allocations to what surveys actually cost when done to international standards. Rebase the national accounts with proper underlying survey infrastructure so the numbers reflect the economy rather than a methodology change.

And invest in PBS's institutional capacity before the next macro crisis makes the data gaps visible again, by which point it will already be too late. Pakistan cannot run a data-driven state, make an honest case for its own economic performance, or design reforms that reach the people they are meant to reach, without a properly funded statistical system. Budget 2026-27 gives PBS Rs 5.41 billion.

The conversation that funding either enables or forecloses is worth considerably more - we need to measure before we govern.

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