Kartik Chundru

The paper’s great too 😅

I love that movie. There’s something very satisfying about watching people do crazy amazing things from the safety of your sofa

Woo!!! @hiwwright.bsky.social bamboozles us with his All of Us mastery!

This is the result of lot of hard work and some brilliance from one of the most talented ECRs I’ve worked with

A very important message which will reduce a lot of noise in aggregate associations, and improve interpretability

What genetic change to Indian wheat led to superior baking in a tandoor?

A naan sense mutation

Modulating splicing in five prime untranslated regions to treat rare haploinsufficient disease Rare genetic disorders collectively impact over 300 million people worldwide, yet around 95% have no specific treatments. For the many rare disorders caused by haploinsufficiency, effective therapies ...

*A new pre-print on increasing gene expression!* 🧬📈

doi.org/10.64898/202...

Our new study defines a distinct #neurogenetic condition arising from recurrent structural variants at 16p13.3 palindrome.

Individuals show progressive ataxia, cognitive decline, and a characteristic MRI pattern with caudate & cerebellar atrophy.

#Genomics #RareDisease 🧵1/3

“Herasight claims to deliver an average gain of six IQ points for a couple with five embryos”
Probably with a sd of 20 😂
Paying £40k for that is insanity

Early Christmas present! Thank you Father Quistmas!🎅

Domain-wide Mapping of Peer-reviewed Literature for Genetic Developmental Disorders using Machine Learning and Gene2Phenotype https://www.medrxiv.org/content/10.1101/2025.11.24.25340871v1

It was a privilege to be part of this important international effort. How should we determine the value of genomics in healthcare?

Please forward this to any you know who could be interested!

The incredible @drghawkes.bsky.social will be leading a course on analysis of genome sequence data, functional annotation of the genome, and using the very, very exciting AlphaGenome tool

Great work Alex and team! Have been following with interest for a while.

I’m still in team “2nd tier test” 😅 but all of your work has made me think about it more.

Do you think you will make much gain using pangenome assembly, in particular for complex gene/regions?

Congrats @hilarycmartin.bsky.social!!

Thank you 🙂 I’m looking forward to reading your flexRV paper and giving it a try!

Rarely in the entire history of science, has QC been a topic of such passion, importance and impact. If only the French and Americans had adopted such rigor when they messed up the design of that multi billion $ telescope because one was using the metric system, the other the imperial system.

hell yes! (another quote for you kartik)

Genomic superstar @chundru.bsky.social taking on fake-news genotypes in >900k individuals. He shows allele-level filtering is rarely suffifient, and makes the brave choice to properly tackle chrX!

We’ll be providing our filtered AoU WGS plink pgens for all registered users: watch this space

Ha! Thanks, I'll file right under "Even reviewer 3 was speechless"

Thank you to other co-authors @carolinefwright.bsky.social, @mnweedon.bsky.social, @timfrayling.bsky.social, and @drarwood.bsky.social, @nihrexeterbrc.bsky.social, biobanks @ukbiobank.bsky.social and All of Us, and all of the participants of the studies

A massive, massive thank you to @hiwwright.bsky.social, @rnbeaumont.bsky.social, @drghawkes.bsky.social who all really drove this project to completion. Without them I would still be twiddling my thumbs shouting to the clouds about QC (I still will, but now you can read about it too!)

GitHub - chundruv/ukbb_pvcf2pgen: UKBB pVCF to plink pgen conversion UKBB pVCF to plink pgen conversion. Contribute to chundruv/ukbb_pvcf2pgen development by creating an account on GitHub.

Using our DNANexus applet it is fast and not too expensive to QC and convert the entire UK Biobank WGS files to pgens! github.com/chundruv/ukb...

And for All of Us v8, we will provide you with the QC’ed pgen files on publication in a public workspace available to registered users.

“Ok fine, but what about the X chromosome, you always forget that”

This time we didn’t ignore the X chromosome! We show that you should pay special attention to non-pseudoautosomal X chromosome where QC should be more lenient for haploid males.

“But Kartik, how do we know the genotypes are wrong?”

Trios! Both cohorts have ~1k parent-offspring trios that were recruited incidentally.

Applying genotype-level QC reduces Mendelian errors by ~60-80% (even in All of Us where they already did genotype-level QC on hom-refs!)

“Bah humbug! How bad could it be?”

After genotype-level QC and a 10% missingness cut-off, we remove ~100 million (~9%) variants!

Most genotypes removed are homozygote reference (which were filtered in All of Us already)

We caution that the released data in UK Biobank and All of Us is not as clean as you may believe!

Here, we show how we determine data quality in WGS data, provide a really fast way of doing so on biobank data, and we will release QC’ed plink files for All of Us upon publication

Genotype-level quality control substantially reduces error rates in population-scale whole-genome sequencing Population-scale whole-genome sequencing data will contain many individual-level genotype errors, even after allele-level quality control (QC). We establish the need for genotype-level QC using UK Bio...

New paper on everyone’s favourite topic, QC!
We show why you should do genotype-level QC on your WGS data

www.biorxiv.org/content/10.1...

Very real quotes about this paper -
“The most exciting, mind-blowing paper of the year!”
“On a par with Fisher 1918”
“I read it every night. Just so beautiful”

Really cool work from @jacquesml.bsky.social and @kash-a-patel.bsky.social 🥳
24% common variant heritability for a rare disease (MODY)!
This very elegantly shows the overlap between MODY and T2D, and hints at some potential MODY phenocopies

New preprint out now! We show polygenic background shapes GCK-MODY clinical presentation. In >1,000 cases, higher polygenic risk increased the chance of exceeding diagnostic diabetes thresholds, highlighting how monogenic & polygenic factors jointly shape disease. #Genetics

The role of untranslated region variants in Mendelian disease: a review - European Journal of Human Genetics European Journal of Human Genetics - The role of untranslated region variants in Mendelian disease: a review

Super excited to share our new review paper - The role of untranslated region variants in Mendelian disease!
www.nature.com/articles/s41...

⌛Just over a week left!

Submit your abstract for the Cardiac Precision Medicine in the 21st Century Conference 🫀

📅 Oct 29–31, 2025 | Toronto

Showcase your research + compete for Best Abstract Award!
🔗 cardiacprecisionmedicine.com

#CardiacPrecision #Genomics #callforabstracts