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Kartik Chundru

@chundru.bsky.social
791 followers 490 following 64 posts

Postdoc at University of Exeter 🇮🇪🇮🇳🇬🇧 Statistical/Computational analyses using any NGS-based data Formerly at Sanger institute working on recessive developmental disorders in DDD

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Reposted by Kartik Chundru
James Fasham @jamesfasham.bsky.social · 16/06/2026
🧬 Leigh Jackson (Exeter) presents multiple papers (see EJHG Special Issue ☝️ ) #ESHG2026 Penetrance of TSC, PCD, OI & RB1 across ~900,000 individuals Careful variant & phenotype curation matters In clinically unselected populations, disease risk can be ⬇️ than traditional estimates. #Genomics
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Kartik Chundru @chundru.bsky.social · 14/06/2026
Whoop! Very proud to see how far Mwenda has come in such a short space of time 🤩
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James Fasham @jamesfasham.bsky.social · 13/06/2026
Caroline Wright (Exeter) sharing fundamental knowledge What does the "average" human genome look like?" >900k 🧬 #UKB / #AllofUs / Genome: 1️⃣ ~4.4–5.5 million variants 2️⃣ 2–3 ClinVar P/LP (mostly AR) 3️⃣ ~62–70 de novo variants 4️⃣ ~1 in 5 people in top 1% of PRS for ≥1 disease
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Caroline Wright @carolinefwright.bsky.social · 12/06/2026
Exeter genomics out in force at #ESHG2026 in Gothenburg! Multiple talks and posters every day...
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Kartik Chundru @chundru.bsky.social · 06/02/2026
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
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Michael Hoffman @michaelhoffman.bsky.social · 10/01/2026
What genetic change to Indian wheat led to superior baking in a tandoor? A naan sense mutation
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Eloise Beer Wells @eloisewells.bsky.social · 10/12/2025
*A new pre-print on increasing gene expression!* 🧬📈 doi.org/10.64898/202...
doi.org
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 ...
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Reposted by Kartik Chundru
James Fasham @jamesfasham.bsky.social · 08/12/2025
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
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Kartik Chundru @chundru.bsky.social · 02/12/2025
Early Christmas present! Thank you Father Quistmas!🎅
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medRxivpreprint @medrxivpreprint.bsky.social · 25/11/2025
Domain-wide Mapping of Peer-reviewed Literature for Genetic Developmental Disorders using Machine Learning and Gene2Phenotype www.medrxiv.org/content/10.1101/202…
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Exeter Rare Disease @rdexeter.bsky.social · 27/11/2025
It was a privilege to be part of this important international effort. How should we determine the value of genomics in healthcare?
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Kartik Chundru @chundru.bsky.social · 17/11/2025
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
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Tim Frayling @timfrayling.bsky.social · 08/11/2025
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.
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Ruby Dawes @ruebenadawes.bsky.social · 10/11/2025
hell yes! (another quote for you kartik)
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Dr Gareth Hawkes @drghawkes.bsky.social · 10/11/2025
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
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Kartik Chundru @chundru.bsky.social · 08/11/2025
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”
biorxiv.org
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...
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Kartik Chundru @chundru.bsky.social · 09/09/2025
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
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Jacques Murray Leech @jacquesml.bsky.social · 11/08/2025
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
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Nechama Wieder @nechamawieder.bsky.social · 04/07/2025
Super excited to share our new review paper - The role of untranslated region variants in Mendelian disease! www.nature.com/articles/s41...
nature.com
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
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SickKids Cardiac Precision Medicine @skcardprecisionmed.bsky.social · 27/06/2025
⌛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
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Žiga Avsec @avsecz.bsky.social · 25/06/2025
Excited to launch our AlphaGenome API goo.gle/3ZPUeFX along with the preprint goo.gle/45AkUyc describing and evaluating our latest DNA sequence model powering the API. Looking forward to seeing how scientists use it! @googledeepmind
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Aparajita Sriram @aparajita-sriram.bsky.social · 04/06/2025
Excited to share the preprint of our paper (my first paper!) looking at limited evidence MODY genes. We use rare variant burden testing and one of the largest MODY cohorts to evaluate the pathogenicity of these genes. This evidence can help inform clinical guidelines in MODY genetic testing!
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Caroline Wright @carolinefwright.bsky.social · 27/05/2025
Last day of #ESHG25 #ESHG2025, make sure to catch two fantastic back-to-back talks from @hls.exeter.ac.uk @drghawkes.bsky.social describing whole genome association analysis and meta-analysis across >500,000 people (Tuesday 11:15 & 11:30, C32)
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Dr Gareth Hawkes @drghawkes.bsky.social · 27/05/2025
Come along today and see me and Harry begin to tackle the exponentially increasing population scale WGS data! #ESHG2025 #ESHG25
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Nicky Whiffin @nickywhiffin.bsky.social · 26/05/2025
The team have all done their job beautifully #proudPI - now it is my turn. Join us in the late breaking session to hear about collaborative work with @gregfindlay.bsky.social on saturation genome editing of RNU4-2 (at 11:30). You will also get to hear the awesome @chundru.bsky.social! #eshg2025
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Caroline Wright @carolinefwright.bsky.social · 26/05/2025
At #ESHG25, make sure to hear the fantastic @chundru.bsky.social speak about characterizing genome-wide de novo mutations in control populations versus rare disease cases (Monday 11:15, C29), part of the work we're doing in paradigmgenomics.org
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Kartik Chundru @chundru.bsky.social · 26/05/2025
I will be talking today in Space 3. The session starts at 10:30, my talk will be at 11:15 Come join if you are interested in de novo mutations, non-coding genome, rare disease, or just up for seeing @nickywhiffin.bsky.social talk about RNU4-2 saturation mutagenesis after me 😂 #ESHG2025
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James Fasham @jamesfasham.bsky.social · 23/05/2025
Thanks Gareth! I'm speaking at Workshops W10 and W19. Also please do see Leigh's poster that has some our data on low penetrance of TS in biobank - keen for feedback! #ESHG2025
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Kartik Chundru @chundru.bsky.social · 23/05/2025
Do come see some of these talks and posters! These are all incredible scientists (and @drghawkes.bsky.social), I can’t recommend them and their research enough #ESHG2025
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Kartik Chundru @chundru.bsky.social · 23/05/2025
I’m really looking forward to #ESHG2025! Hopefully it goes better than my start, I dropped my laptop bag first thing this morning 😅 luckily no damage
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deciphergenomics.bsky.social @deciphergenomics.bsky.social · 07/05/2025
Human Developmental Cell Atlas (HDCA) expression data is now displayed. Expression is displayed in 12 sections of a 6-7 post-conception week human embryo, alongside a sagittal view which displays the region of the embryo represented by each section @mhaniffa.bsky.social
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Isaac García @isaacgs94.bsky.social · 16/05/2025
It's finally out people ✅🗞️! Check out the final version of our work exploring factors influencing the germline mutation rate and spectra on ~10,000 WGS family trios 🧬👨‍👩‍👦! www.nature.com/articles/s41...
nature.com
The impact of ancestral, genetic, and environmental influences on germline de novo mutation rates and spectra - Nature Communications
Here the authors analyze de novo mutations in >10,000 parent-offspring trios and find that ancestry and smoking independently associate with mutation rate, but that common genetic variants likely c...
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Kartik Chundru @chundru.bsky.social · 24/04/2025
Only 3 days until the deadline! Please pass along to anyone you feel would be interested
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Kartik Chundru @chundru.bsky.social · 18/04/2025
I thought I’d check what was new on Bluesky 😳 this is seriously f***ed up! Sending love to my US colleagues ❤️
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Nicky Whiffin @nickywhiffin.bsky.social · 11/04/2025
Greg immediately hypothesised that these might be recessive variants, evident only as we used a haploid cell line. This led us to identify a novel NDD associated with biallelic RNU4-2 variants, with a phenotype distinct from ReNU 🤯 (companion manuscript fully describing this coming soon!) 9/12
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Nicky Whiffin @nickywhiffin.bsky.social · 11/04/2025
🚨I could not be more excited to share our new preprint on saturation genome editing of the small nuclear RNA (snRNA) RNU4-2: www.medrxiv.org/content/10.1... A super fun collaboration with incredible duo @gregfindlay.bsky.social @joachimdejonghe.bsky.social from @crick.ac.uk 🧬🖥️🩺 🧵1/12
medrxiv.org
Saturation genome editing of RNU4-2 reveals distinct dominant and recessive neurodevelopmental disorders
Recently, de novo variants in an 18 nucleotide region in the centre of RNU4-2 were shown to cause ReNU syndrome, a syndromic neurodevelopmental disorder (NDD) that is predicted to affect tens of thous...
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Florian Privé @privefl.bsky.social · 10/04/2025
✅ In this paper, I used the UK Biobank to define 18 reference worldwide populations, and provided a method to easily infer ancestry proportions of individuals from your study more accurately. Please have it a try! Paper: doi.org/10.1093/bioi... Tutorial: privefl.github.io/bigsnpr/arti...
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James Russ-Silsby @jamesr-s.bsky.social · 04/04/2025
There are fewer than 10 documented genetic causes of Transient Neonatal Diabetes (TNDM) and now PAX4 is one of them! Really proud of this collaborative work done between the Neonatal Diabetes Research Team at Exeter and the Translational Genomics of Diabetes Lab in Stanford.
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Kartik Chundru @chundru.bsky.social · 04/04/2025
Come join us! I cannot recommend Exeter enough as a place to live and work @exeter.ac.uk! You’ll be joining a very friendly, collaborative, supporting environment. With the added bonus of working on ground-breaking research
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Jeff Spence @jeffspence.github.io · 28/03/2025
A really nice paper by @drghawkes.bsky.social et al. argues that rare and common genetic associations converge on the same genes. While this seems at odds with our recent work about how burden tests and GWAS prioritize different genes, our results agree (🧬🧪🧵 1/6) www.biorxiv.org/content/10.1...
biorxiv.org
Whole-genome sequencing analysis of anthropometric traits in 672,976 individuals reveals convergence between rare and common genetic associations
Genetic association studies have mostly focussed on common variants from genotyping arrays or rare protein-coding variants from exome sequencing. Here, we used whole-genome sequence (WGS) data in 672,...
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Harriet Dashnow @hdashnow.bsky.social · 26/03/2025
The strchive.org paper is out!! The paper describes STRchive as a resource to improve the diagnosis of tandem repeat disorders, then goes beyond it to consider what can be learned about childhood onset and population prevalence of these diseases. 🖥️ 🧬 link.springer.com/article/10.1...
link.springer.com
STRchive: a dynamic resource detailing population-level and locus-specific insights at tandem repeat disease loci - Genome Medicine
Approximately 8% of the human genome consists of repetitive elements called tandem repeats (TRs): short tandem repeats (STRs) of 1–6 bp motifs and variable number tandem repeats (VNTRs) of 7 + bp moti...
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Caroline Wright @carolinefwright.bsky.social · 27/02/2025
Fantastically useful clinically-curated resource of structured monogenic gene-disease associations, including inheritance and disease mechanisms.
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Mallory Freeberg @malloryfreeberg.bsky.social · 27/02/2025
#standards, #mechanisms, & #identifiers - oh my! Just in time for #RareDisease Day, the @gene2phenotype.bsky.social website has a fresh look & new features to improve access to gene-disease models. 🧬💻 👉 Updated website: www.ebi.ac.uk/gene2phenoty... 👉 Why it matters: www.ebi.ac.uk/about/news/u...
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G2P @gene2phenotype.bsky.social · 27/02/2025
We have launched an updated Gene2Phenotype website with a fresh new look. We now support more detailed disease mechanism information in our expert-curated gene-disease models. Available at www.ebi.ac.uk/gene2phenotype.
ebi.ac.uk
Gene2Phenotype
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Sasha Gusev @sashagusevposts.bsky.social · 26/02/2025
We finally have some well-powered whole-genome heritability estimates, including a quasi-behavioral trait (BMI). For height, ~89% of the heritability estimated to reside in common variants. For BMI and WHR, ~100% estimated in common variants. www.biorxiv.org/content/10.1...
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Kartik Chundru @chundru.bsky.social · 26/02/2025
Very happy to have this preprint out 😀 It's a testament to the amazing collaboration ongoing at the @exeter.ac.uk! I really loved working with this fantastic team and I think we have some very interesting findings which will be of interest to the wider research community! More to come from us soon!
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Kartik Chundru @chundru.bsky.social · 24/02/2025
Lovely work from @drghawkes.bsky.social and @rnbeaumont.bsky.social, it was great to be involved in. Just to highlight this part which is new since the preprint. This will be important to consider for interpretation of rare variant burden test results!
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Dr Gareth Hawkes @drghawkes.bsky.social · 24/02/2025
Excited to finally share that our paper looking at the effect of rare non-coding variants using WGS on circulating protein levels in the UKB has been released in Nature Genetics @naturegenet.bsky.social! We now analyse the full 3,000 circulating proteins in all 50,000 individuals rdcu.be/ea16i
rdcu.be
Whole-genome sequencing analysis identifies rare, large-effect noncoding variants and regulatory regions associated with circulating protein levels
Nature Genetics - Rare variant association analysis of plasma proteins using whole-genome sequencing data in 54,306 individuals in the UK Biobank demonstrates that combining both single-variant and...
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kiki 🏳️‍⚧️🏳️‍🌈🧬 @kiki-omics.bsky.social · 21/02/2025
Super excited to introduce our new study, now available as a preprint: tinyurl.com/2hv97yb4 We profiled circulating cell-free DNA during sepsis to understand why it increases >40-fold during disease. We assess cfDNA methylomes, fragmentomes, and nucleosome footprints. (1/3)
A graphical representation of our experimental design. At the top, we see an illustration of a group of people (31 sepsis cases and 7 controls), from whom blood samples are being taken and cell-free DNA isolated. This DNA is then chemically treated to profile all methylated CpG sites. Finally, the diagram shows how this sequencing data is used to derive information on not only DNA methylation, but also cfDNA fragmentation, and nucleosome positioning.
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Rachel Freathy @rmfreathy.bsky.social · 19/01/2025
So happy to see this published in NatComms! tinyurl.com/yc66amvu Rare variant assocs with birth weight identify 9 genes. Insights into links between earlygrowth & later metabolic health. Great collabs between teams Exe&Camb. Amazing resources of UKB & deCODE made it possible.
tinyurl.com
Rare variant associations with birth weight identify genes involved in adipose tissue regulation, placental function and insulin-like growth factor signalling - Nature Communications
An exome-wide association study for fetal and maternal rare deleterious variants affecting the normal variation in birth weight identifies nine genes involved in adipose tissue regulation, placental f...
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