ubaid1

Just your average Ali :p

[Veera Rajagopal  @doctorveera]

Pakistan Genomic Resource (PGR), founded by Danish Saleheen, is the world's largest genetic database of human knockouts. It has been quietly building since 2017, from 10,000 individuals (Saleheen et al. Nature 2017) to nearly 200,000 today.

A new paper in Nature by Koch et al. reports a new analysis of 173,303 Pakistanis from PGR, offering genetic insights from natural inbreeding experiments in humans.

Koch et al. Nature 2026
https://t.co/Uk9YaeN1Ev

In biology, to understand what a gene does, you delete it, a standard experiment. Knock out the gene in a mouse and see what breaks: organ fails, behaviour changes, animal dies. Thirty years of biology built this way. It works, until it doesn't. Because, you know, mice are not humans.

To know the function of a gene in humans, you need a similar experiment. But that's unethical, you cannot deliberately delete a gene in a human. Except you don't have to, because nature has already been doing that experiment.

Occasionally, a person inherits a broken copy of a gene from both parents and is born with no working version at all--a human knockout. The problem is finding them. In most of the world's populations, where mating is largely random, these events are nearly invisible. For a gene-inactivating variant at 0.1% frequency, you'd expect one homozygous individual in every million people.

That math collapses in populations like Pakistan, where consanguineous marriage has been practised for centuries. In first-cousin marriages, the odds of observing a human knockout for the same 0.1% variant rise to roughly 1 in 16,000, a 63-fold enrichment. And the rarer the variant, the larger the advantage: ~630-fold for a 0.01% variant, ~6,300-fold for a 0.001% variant. The variants too rare to ever be seen in European biobanks become findable here.

Sequencing more than 170,000 individuals from highly consanguineous communities, the authors report a mind blowing statistic: at least one living human knockout was observed for 6,476 genes, which is nearly 1/3rd of the entire protein-coding genome!

What do we find when we finally have the human knockouts?

Studying the phenotypes in the human knockouts helps us confirm or refute our understanding of the gene's function based on animal studies. A few examples I highlight below.

PRDM9
PRDM9 might be one of the most popular genes among animal biologists. It encodes a protein that controls where chromosomes break and recombine during sperm and egg formation. Deleting the gene has caused infertility in every animal. PRDM9 was classified as the first hybrid sterility gene in vertebrates, so fundamental that crosses between mouse species with different PRDM9 alleles can't produce a fertile offspring. PGR now has 4 human PRDM9 knockouts : three women, one man. All fertile, with 2 to 7 children each. A 14-year biological fact, overturned by four families in Pakistan.

LRRK2
LRRK2 is a well-established Parkinson's disease risk gene. Activating mutations in LRRK2 are among the most common risk factors for Parkinson's. LRRK2 is a therapeutic target with many companies exploring ways to switch off this gene in the brain to treat Parkinson's. Large-scale sequencing studies have found individuals with partial loss of LRRK2, who did not show any concerning health issues, predicting adverse effects of LRRK2 inhibition in humans. Animal knockouts though warned of kidney damage. Now PGR has two LRRK2 knockouts, both with kidney disease, confirming animal studies.

RXFP1
RXFP1 encodes the receptor for a pregnancy hormone called relaxin, which has long been studied in rodents. Animal studies suggested it played a critical role in cardiovascular adaptation and connective tissue remodelling, fuelling relaxin-targeted drug development, which failed in late-stage trials. PGR found 16 RXFP1 knockouts, expanded to 26 via recall-by-genotype, all tested with cardiac imaging. None had consistent cardiovascular or reproductive deficits, retrospectively explaining the failure of relaxin-targeted drug programmes that might have spent millions of dollars. Mouse physiology failed to inform humans in the case of relaxin.

Gene constraint insights
Existing large-scale biobanks are predominantly European-based outbred populations, which shaped our understanding of gene constraints largely based on intolerance to partial loss of function. Now PGR, a South Asian-based cohort enriched for consanguineous communities, is beginning to offer insights into gene constraints based on intolerance to complete loss of function.

PGR showed that nearly 1/3rd of human genes tolerate complete loss of function. As much as the genes for which knockouts were found, the genes for which knockouts weren't found can offer biological insights.

The authors find genes depleted for knockouts in PGR are enriched for genes essential for cell survival, known Mendelian disease genes (both dominant and recessive) and genes broadly expressed across human tissues.

A fascinating insight is significant enrichment for knockouts in tissue-specific genes (OR=2.39). Human knockouts confirm what drug developers have always thought: tissue-specific genes are much safer therapeutic targets than broadly expressed genes.

The above insight should be read with caveats. The sample size of PGR is small, hence not saturated for human knockouts. It's likely the number of genes will increase as the sample size grows. There is a survivorship bias, like any other volunteer-based cohort. Absence of a gene knockout here doesn't mean biological impossibility. It means incompatibility with being a 'healthy' adult volunteer. If you build a cohort based on a hospital-based pediatric rare disease South Asian cohort, you'd expect to see knockouts that never appeared in PGR.

South Asian populations represent nearly a quarter of humanity, yet they have been largely absent from the genomic revolution. PGR shows what absence has been costing the field: overturned biological assumptions, failed trials, missed targets. The biology was always there. We just weren't looking in the right place.

[a @Abbasayy]

Imran Khan's reply to every question about his future plans

[SyncOsint @factwatchORG]

PM Imran Khan narrates entire conspiracy
involving US embassy, journos, turncoats
#امپورٹڈ_حکومت_نامنظور

[Mudassar Ali @Doct0r007]

These 2 r so relatable
#امپورٹڈ_حکومت_نامنظور
#SupremeCourtofpakistan

[muhammad Bilal @muhamma78018469]

Voice of every Pakistani
#SupremeCourtofpakistan
#ImportedHukumatNaManzoor
#امپورٹڈ_حکومت_نامنظور

[محمد سلمان شفیق @salmanchand779]

Remember, in a country where children are so conscious, they will be as conscious as their youth, so you need to think, and this is a matter of great concern to you
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#امپورٹڈ_حکومت_نامنظور

[syed arslan hussain @syedarslanhus14]

Brave leader Imran Khan
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[CoinMarketCap @CoinMarketCap]

Moment of silence for those who told their family members to get into crypto over the holidays 🤧

[z @bus_kerdou]

Fav if you’re a 29+ year old Pakistani who, as a teenager, believed that once a “a few generations die out” Pakistan ke haalaat behtar ho jayein gay. Camera ki taraf dekh kar haath hilaa dain.

[ubaid1 @ubaid1]

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[ubaid1 @ubaid1]

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[ubaid1 @ubaid1]

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[RACA @RACA_3]

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[RACA @RACA_3]

Metamon Game has over 10k daily active users
300 Metamon Eggs will be airdropped

Follow @RadioCacaNFT @USMverse @USMchain @BinanceChain
Like, RT, tag 3 friends #RACA #BSC #Metamon
Join Discord https://t.co/xJrOM9QTwb
Join TG https://t.co/vkn0uiENRi
More https://t.co/7mHCTTyusD

[RT @RT_com]

Michael Lofthouse, founder & CEO of tech firm Solid8, has issued a groveling apology after his racist tirade in a California restaurant went viral

Since being identified, he deactivated his LinkedIn & Twitter accounts, telling UK press: ‘My behavior in the video is appalling'

[ubaid1 @ubaid1]

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[RT Sport @RTSportNews]

😳 He's tested positive for coronavirus for a FOURTH time...

https://t.co/niIIuU724R

[Global Times @globaltimesnews]

Chinese tech giant #Huawei has again proved its technology strength by helping build #5G stations with China Mobile high on Mount Qomolangma, also known as #MountEverest, the world's highest peak. https://t.co/JYCJYaMC16

[Abdulmalik Koya @abdulmaleekkoya]

DON’T BE LIKE BILL!

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[Maheeda 💕 @Maheeda__miz]

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The video below will show you what i really mean.

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[RT @RT_com]

Doctors & nurses on frontline in battle against #COVID19, says #Putin as he gives them pay rise & same benefits as military

MORE: https://t.co/mTvqiJBeOs