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Aoxing Liu

@aoxing2.bsky.social
365 followers 394 following 30 posts

postdoc with Mark Daly at Broad Institute & MGH - curious about (large) chromosome alterations & (deep) human pedigrees + immunity, cancer & their interplay :)

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Reposted by Aoxing Liu
Jack Kosmicki @jakphd.bsky.social · 25/06/2026
After 4 years, it's rather nice to finally present our work on genetic's model trait, height, in >1.4M WES/WGS samples (826k discovery; led by Adam Locke & Goncalo Abecasis where we found (amongst many other things) 207 genes (P<1.75e-9). A thread of findings below⬇️ www.medrxiv.org/content/10.6...
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Aoxing Liu @aoxing2.bsky.social · 12/06/2026
If you’re at #ESHG2026, don’t miss Yining’s talk tomorrow 11:00 (Session C03)!!! We’ve got MORE to share than at our ASHG talk last year. Mark & I can’t make it this year - but please do catch up and say hi to Yining if you’re there!!! @finngen.bsky.social @eshg.bsky.social
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Reposted by Aoxing Liu
Konrad @konradjk.bsky.social · 13/05/2026
🧬 New preprint! We present an All by All analysis in All of Us: common and rare variant association testing across 392,030 whole genomes and 3,602 phenotypes. 1.337 trillion tests, ~50k significant signals, all publicly browseable. www.medrxiv.org/content/10.6...
medrxiv.org
Systematic common and rare variant association testing in 392,030 whole genomes in All of Us
Large-scale genome-wide association studies (GWAS) and rare variant association studies (RVAS) from population biobanks provide valuable resources for gene discovery in complex human traits. We presen...
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Reposted by Aoxing Liu
🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · 06/05/2026
Aoxing @aoxing2.bsky.social gave a great talk at #BoG2026 (even more considering it was last minute promoted to a talk!) on studying sex chromosome dosage thanks to available biobank data from rare but tolerated sex chromosome trisomies Builds upon doi.org/10.1016/j.aj... @cshlmeetings.bsky.social
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Reposted by Aoxing Liu
Masahiro Kanai @masakanai.bsky.social · 01/12/2025
Excited to share our new FinnGen single-nucleus multiome preprint! 🧬 We profiled ~10M PBMCs (snRNA-seq + snATAC-seq) from 1,108 Finnish donors to map how genetic variants drive complex disease through chromatin and gene regulation 🧵👇 🔗 Link: www.medrxiv.org/content/10.1...
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Aoxing Liu @aoxing2.bsky.social · 24/10/2025
If you’re looking for highly heritable quantitative traits (beyond height!) to test your new methods, these “lab values” could be your next model traits!! We did so in our pedigree-BLUP work: we estimated family-based h2 & compared it to SNP h2 to clarify the different concepts of heritability!!
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Aoxing Liu @aoxing2.bsky.social · 24/10/2025
New from FinnGen!! 🚀🚀🚀 FinnGen just released GWAS summary statistics for 383 lab measurements (OMOPIDs) - each based on ≥1,000 participants!! All results are open for browsing & download: 👉 labvalues.finngen.fi. 🧬🧬🧬 Have fun!! 🏄🏄‍♀️🏄‍♂️
labvalues.finngen.fi
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Reposted by Aoxing Liu
Nature Reviews Cancer @natrevcancer.nature.com · 20/10/2025
Comment🚨 Large biobank projects like #FinnGen help in uncovering genetic factors that influence cancer risk and outcomes, enhancing risk prediction & biomarker and drug target discovery. @finngen.bsky.social @dalygene.bsky.social @aoxing2.bsky.social 📖 👇
bit.ly
Unlocking the potential of FinnGen to advance cancer research - Nature Reviews Cancer
Large biobank projects such as FinnGen have enabled systematic searches for inherited factors that causally influence a wide range of human traits, including cancer risk and outcome. These explorations provide genetic insights for various aspects of cancer research, including improved risk prediction, enhanced biomarker and drug target discovery, and personalized medicine.
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Aoxing Liu @aoxing2.bsky.social · 17/10/2025
A traditional "Comment" typically wouldn’t include such a "complicated" figure - we have to follow journal guidelines (=delete it from the paper). However, we’re free to share the full version with you here!! For those who think in pictures (myself included), I hope you find it clear & helpful! 🫶
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Aoxing Liu @aoxing2.bsky.social · 16/10/2025
Excited (😁) to share a commentary on @finngen.bsky.social & cancer research, co-written with Mervi Aavikko & @dalygene.bsky.social!! (View-only full text -> rdcu.be/eLlJs)
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Aoxing Liu @aoxing2.bsky.social · 14/10/2025
Join Jesse & me for a 🌟 #ASHG2025 Featured Symposium!! "Decoding Human Aging: From Single-Cell Resolution to Population-Scale Insights" ⏰ Oct 17, 8:30-10:00 AM 🏡 258ABC, Level 2 With a fantastic ✨ speaker lineup - @albarmeira.bsky.social & Albert (Kejun) & Giulio & @austinargen.bsky.social! 2/n
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Aoxing Liu @aoxing2.bsky.social · 14/10/2025
Happy (😀) to invite you to our Talk/Featured Symposium/Poster/Booth at #ASHG2025!! ⏰ Oct 15, 1:30 -1:45 PM 🏡 258ABC, Level 2 I'll be giving a talk on sex chromosome trisomies (XXY, XYY, XXX) - and the surprising new biology of chromosomes X and Y!! Link: meetings.ashg.org/event/ASHG25... 1/n
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Reposted by Aoxing Liu
FinnGen @finngen.bsky.social · 10/10/2025
We’re getting ready for an exciting week at #ASHG2025 in Boston! Come meet the FinnGen team at booth 147 - we’ll be sharing updates and showcasing new public resources and tools. Plus, don’t miss the various presentations featuring FinnGen results across the program! www.finngen.fi/en/meet-finn...
finngen.fi
Meet FinnGen at the ASHG 2025! | FinnGen
Results based on the FinnGen data are presented in almost 40 talks or posters during the 2025 Annual Meeting of the American Society of Human Genetics (ASHG) in Boston, October 14-18. We also have a b...
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Reposted by Aoxing Liu
Inigo Martincorena @imartincorena.bsky.social · 08/10/2025
Our latest work is out in Nature today. In this paper, we introduce an improved version of NanoSeq, a duplex sequencing protocol with <5 errors per billion bp in single DNA molecules, and use it to study the somatic mutation landscape of oral epithelium in >1000 people www.nature.com/articles/s41...
nature.com
Somatic mutation and selection at population scale - Nature
A new version of nanorate DNA&nbsp;sequencing, with an&nbsp;error rate&nbsp;lower than five errors&nbsp;per billion base pairs&nbsp;and compatible with whole-exome and targeted capture, enables epidemiological-scale studies of somatic mutation and selection&nbsp;and&nbsp;the generation of high-resolution&nbsp;selection&nbsp;maps across coding and non-coding sites for many genes.
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Reposted by Aoxing Liu
Yun S. Song @yun-s-song.bsky.social · 22/09/2025
We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics. www.biorxiv.org/content/10.1... (1/n)
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Aoxing Liu @aoxing2.bsky.social · 21/08/2025
Thanks, Cristian!! 😄😄😄
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Aoxing Liu @aoxing2.bsky.social · 21/08/2025
Our trisomy work is now online! 🚀 Got curious after reading our short PheWAS paper? 👀 Catch me 🌠 & my talk 🎤 this October at #ASHG25 in Boston! Yes, I am still endlessly curious about sex chromosome aneuploidies - whether it's somatic (X/Y loss) or germline (trisomies)!! 💘
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Aoxing Liu @aoxing2.bsky.social · 11/06/2025
And Figure 1 in the preview summarizes everything so nicely - way better than we authors could!! Preview: www.cell.com/cell-genomic... Original research article: www.cell.com/cell-genomic...
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Aoxing Liu @aoxing2.bsky.social · 11/06/2025
And, the figure one you generated is so informative!!
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Aoxing Liu @aoxing2.bsky.social · 11/06/2025
Thanks @struangrant.bsky.social ‬and @agacita.bsky.social for seeing the uniqueness of our work and guiding others to understand it better!! Really appreciate your vision and insight!!
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Aoxing Liu @aoxing2.bsky.social · 11/06/2025
Wow!! Big thanks for the very lovely preview!! 🫶🫶🫶 TOO MANY analyses -> very DIFFERENT feedback on (several of) our submissions - some thought it was too lengthy, others considered the design creative, rigorous. Perhaps no need to do standard analyses if the data/question itself is not standard...
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Aoxing Liu @aoxing2.bsky.social · 26/05/2025
Thanks to the @finngen.bsky.social team for years of effort 🫶 in making it a unique resource for genetic discovery, and congratulations to FinnGen researchers (including us 😉) for utilizing the resources smartly!!
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Aoxing Liu @aoxing2.bsky.social · 24/05/2025
Hi - Excited to share our two talks at @eshg.bsky.social about @finngen.bsky.social! Because of ... I cannot join in person, but I will answer your questions online (or write to me)! 🧬 Feiyi & Zhiyu are in Milan now; discuss the BLUP work with them (if you can catch them❤️‍🔥)! Enjoy the conference!
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Aoxing Liu @aoxing2.bsky.social · 02/05/2025
8/n Parental T1D PGS is a strong predictor of T1D risk in children. About parental PGSs of other AIDs - not adding too much to the prediction, given the high accuracy of T1D PGS. PGS vs family history? High parental PGSs are usually more informative than a diagnosis of T1D in the mother or father.
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Aoxing Liu @aoxing2.bsky.social · 02/05/2025
7/n People with AIDs are less likely to have children - for many reasons, including fear of transmitting diseases to offspring. By estimating T1D risk for their children, couples can have informed family planning. Also, children at high risk can benefit from targeted screening & early prevention.
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Aoxing Liu @aoxing2.bsky.social · 02/05/2025
6/n With pTDT, we see 2 main patterns for parent AID -> offspring T1D inheritance: Pattern 1 – Overtransmission of both HLA & non-HLA PGSs for parental T1D, HYPO, RA, SLE. Pattern 2 – Transmission occurs only for HLA: overtransmission for parental CD & psoriasis, undertransmission for IBD & MS.
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Aoxing Liu @aoxing2.bsky.social · 02/05/2025
5/n But our original curiosity is about parents & children... We can run polygenic transmission disequilibrium tests (pTDT) with AID HLA & non-HLA PGS in FinnGen trios! A reminder - pTDT checks if AID risk variants are passed on more or less to children with T1D compared to what would be expected.
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Aoxing Liu @aoxing2.bsky.social · 02/05/2025
4/n Now, let's revisit the question of the shared genetic background! 🧬🧬🧬 Overall, genetic analyses are consistent with epidemiological findings. For example, for HYPO, CD, RA, both HLA & non-HLA show positive effects. However, for MS & IBD, non-HLA has no effect, while HLA has protective effects.
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Aoxing Liu @aoxing2.bsky.social · 28/04/2025
3/n Genetic correlation is straightforward but remember HLA - largely impacting T1D & other AIDs - is excluded by LDSC. If genetic correlation is a genome-wide non-HLA measurement, how can we get HLA back into the game? We built a within-sample HLA PGS with weighted ridge classifiers in FinnGen.
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Aoxing Liu @aoxing2.bsky.social · 28/04/2025
2/n To what extent do the identified epidemiological associations result from genetics?🧬🧬🧬 Let’s download some summary stats and estimate some genetic correlations (quickly). It looks not too bad - if we put the plot of epidemiological analysis aside for comparisons.
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Aoxing Liu @aoxing2.bsky.social · 28/04/2025
1/n Which parental autoimmune diseases (AIDs) are associated with T1D in offspring? With 14,571 trios having T1D-affected children and 43,713 matched control trios (1:3) in Finnish nationwide registers FinRegistry, we identified 9 AIDs associated with increased risk of T1D in offspring.
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Aoxing Liu @aoxing2.bsky.social · 26/04/2025
Why @finngen.bsky.social & why T1D? 1⃣ Finland has the world’s highest incidence of T1D. 2⃣ National healthcare data has been collected for decades -> disease status available for 2 generations. 3⃣ FinnGen genotyped 1/10 of the population + family-based legacy cohorts -> 1.2K T1D genotyped trios.
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Aoxing Liu @aoxing2.bsky.social · 25/04/2025
Type 1 diabetes (T1D) and other autoimmune diseases often co-occur in families. Leveraging data from 12.6K genotyped trios in @finngen.bsky.social, our work - online today in Cell Genomics - studied the transmission of parental autoimmune diseases on T1D in offspring. www.cell.com/cell-genomic...
cell.com
Effects of parental autoimmune diseases on type 1 diabetes in offspring can be partially explained by HLA and non-HLA polymorphisms
Leveraging Finnish nationwide multi-generational registers and the biobanks of FinnGen, Wang, Liu, et al. investigated the effect of parental autoimmune diseases on offspring T1D. Their creative and r...
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Aoxing Liu @aoxing2.bsky.social · 25/03/2025
Join us April 8-9 for @geneticssociety.bsky.social Spring Symposium on Cancer Genetics!! 🧬 I will present our work on #mCAs & #solid_tumors in @finngen.bsky.social. Register link: learning.ashg.org/products/202... Excited to connect with you virtually months before the Boston annual meeting!! 🫶
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Aoxing Liu @aoxing2.bsky.social · 19/02/2025
Fascinating research & dataset - the N of embryos is so impressive!!
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Aoxing Liu @aoxing2.bsky.social · 06/02/2025
Thanks Jack!!
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Aoxing Liu @aoxing2.bsky.social · 06/02/2025
Thanks Shai for posting our trisomy work!! :)
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Aoxing Liu @aoxing2.bsky.social · 06/02/2025
Thanks @jakphd.bsky.social‬ for the nice introduction about our trisomy work!!! 🫶🫶🫶
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