Jeffrey Pullin

Jeffrey Pullin

@jeffreypullin.bsky.social

PhD Student, MRC Biostatistics Unit University of Cambridge Gates Cambridge Scholar Bioinformatics, genetics, single-cell, statistics Australian 🇦🇺

201 followers323 following52 posts

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Jeffrey Pullin reposted

I'll be at #ASHG2026 this year! I'm presenting some recent work (with @huishengzhu.bsky.social) on extracting all the information we can out of rare-variant burden test statistics for downstream meta-analysis. Catch me at poster 8357F to talk about the project or stat gen / pop gen.

Jeffrey Pullin reposted

Very excited to be heading to Montreal for #ASHG26 next week! Come find me at poster board 8448F to talk about scalable single-cell eQTL mapping

Jeffrey Pullin reposted

Out now in Nature! Genetic analysis of the largest single-cell dataset of Inflammatory Bowel Disease (IBD)-relevant tissues nominates effector genes and cell types at over half of known IBD loci, including 74 for which this is the first candidate effector gene 🖥️🧬 www.nature.com/articles/s41...

nature.comCell-type-resolved genetic variation shapes inflammatory bowel disease risk - NatureSingle-cell mapping of cis-expression quantitative trait loci in inflammatory bowel disease revealed distal, enhancer-enriched variants detected at the cell-type level more frequently co-loc...

Overall, we see large, single-cell studies as crucial for closing the colocalisation gap. We also noticed that many GWAS signals colocalise with multiple eQTLs, and further analyses suggested that this is due to co-regulation. Check out the paper for all the details!

tinyurl.com/reuxynmc Very excited to see this work I was a small part of published! We analysed two large scale colocalisation datasets: OpenTargets data and an analysis of immune-mediated disease GWAS/immune cell eQTLs seeking to understand the "colocalisation gap". Some highlights:

journals.plos.orgDesign and interpretation of eQTL-GWAS colocalisation studies: Lessons from a large-scale evaluationAuthor summary Most of the genetic variants associated with complex traits are located outside genes, limiting functional interpretation. Genetic colocalisation helps identify candidate causal genes b...

1) with current data we can colocalise a substantial fraction of GWAS signals: 34% in the IMD/immune cell analysis and 50% in OpenTargets. GWAS signals that were closer to genes and were more common were more likely to colocalise

2) larger eQTL datasets found more colocalisations and enable the detection of lower MAF eQTLs but 3) higher resolution eQTLs identified in single-cell datasets are more likely to colocalise.

Jeffrey Pullin reposted

My last piece of work at the Wallace group. Please check it out and let us know what you think! 😀Thanks @jeffreypullin.bsky.social for summarising it!

Jeffrey Pullin@jeffreypullin.bsky.social

tinyurl.com/reuxynmc Very excited to see this work I was a small part of published! We analysed two large scale colocalisation datasets: OpenTargets data and an analysis of immune-mediated disease GWAS/immune cell eQTLs seeking to understand the "colocalisation gap". Some highlights:

Jeffrey Pullin reposted

tinyurl.com/reuxynmc Very excited to see this work I was a small part of published! We analysed two large scale colocalisation datasets: OpenTargets data and an analysis of immune-mediated disease GWAS/immune cell eQTLs seeking to understand the "colocalisation gap". Some highlights:

journals.plos.orgDesign and interpretation of eQTL-GWAS colocalisation studies: Lessons from a large-scale evaluationAuthor summary Most of the genetic variants associated with complex traits are located outside genes, limiting functional interpretation. Genetic colocalisation helps identify candidate causal genes b...

Jeffrey Pullin reposted

Jeffrey Pullin reposted

🧬 New preprint: "The Human Pleiotropic Map of GWAS Associations and Therapeutic Implications" Why do some genetically supported drug targets succeed in the clinic while others fail? Across 100,526 GWAS, the same evidence flags constrained gene functions rarely safe to modulate.

Jeffrey Pullin reposted

The Open Targets Platform spring 🌼 release is out — and this one marks the beginning of something we've been building towards for a while.

Jeffrey Pullin reposted

Happy to share new manuscript I completed with @ee-reh-neh.bsky.social & @davisjmcc.bsky.social back in Melbourne. The work originally conceived by @ijbeasley.bsky.social focuses on how we can reconcile and meta-analyse eQTL studies across studies cohorts and ancestries. doi.org/10.64898/202...

doi.orgPower is a major confounder in the analysis of cross-ancestry 'portability' in human eQTLsThe phenotypic effects of germline variants are often mediated through gene regulation. Expression quantitative trait loci (eQTLs) are genetic variants associated with changes in gene expression. Understanding how eQTLs vary across populations is essential for characterising the genetic and regulatory drivers of trait diversity. Meta-analysing eQTL studies from multiple populations enables more robust detection of eQTLs and can reveal regulatory mechanisms shaped by population-specific environmental or ancestry-related factors. However, across the multi-ancestry eQTL literature, a wide range of methods have been used to quantify eQTL portability across ancestry groups. Because different studies employ different portability metrics, it is challenging to form a coherent view of the regulatory landscape across populations. In this work, we analyse eQTL summary statistics from ten datasets matched on tissue type and sequencing technology. We compare portability metrics used previously and show that they can yield markedly different patterns of apparent regulatory conservation or divergence. We then examine the statistical determinants of portability across metrics and demonstrate that sample size, minor allele frequency, and linkage disequilibrium are major drivers of the observed differences in eQTL portability across studies. These findings highlight that differences in statistical power stemming from factors such as population size and allele frequency must be accounted for when evaluating eQTL portability. To address this issue, we introduce a new approach designed to correct for these factors when calling eQTL portability. Finally, we show that empirical Bayes multivariate adaptive shrinkage provides a powerful framework for meta-analysing multiple eQTL studies, with the ability to pool signals across populations to produce more robust effect-size estimates within each population. ### Competing Interest Statement The authors have declared no competing interest. National Health and Medical Research Council, https://ror.org/011kf5r70, Ideas Grant 2020501, Investigator Grant 1195595
Irene Gallego Romero@ee-reh-neh.bsky.social

Finally, today's offering! www.biorxiv.org/content/10.6... This began life as a very different project which failed because we couldn't agree on defining eqtl sharing across cohorts. So two young members of the lab dug deeply into this - first @ijbeasley.bsky.social, then @patrickgibbs.bsky.social

Very excited to see this work be the first to use the quasar method for eQTL mapping!

Irene Gallego Romero@ee-reh-neh.bsky.social

First, a couple of weeks ago: www.biorxiv.org/content/10.6... Single cell RNAseq on blood from 200 donors across 4 sites in Indonesia spanning regional axes of genetic and environmental diversity. This is one of very few scRNA data sets from the Global South, including urban and rural settings.

Jeffrey Pullin reposted

Hi yes I will have more to say about this in a few hours but please enjoy this paper. It's been a huge labour of love and effort for the last four years, and a significant part of our research efforts, and I'm so so so thrilled it's finally ready to share. Tldr: scRNA-seq in Indonesia hard but fun

bioRxiv Genomics@biorxiv-genomic.bsky.social

Ancestral and environmental diversity shape the immune landscape in Indonesia https://www.biorxiv.org/content/10.64898/2026.02.15.704933v1

Jeffrey Pullin reposted

Delighted to present Latent Interaction Variational Inference (LIVI), a framework for trans-eQTL mapping at single-cell resolution that I developed during my PhD together with colleagues from @steglelab.bsky.social 1/n

bioRxiv Genomics@biorxiv-genomic.bsky.social

Mapping trans-eQTLs at single-cell resolution using Latent Interaction Variational Inference. https://www.biorxiv.org/content/10.64898/2026.02.04.703363v1

Jeffrey Pullin reposted

New preprint alert: we use sign errors as a test of how well TWAS works. Very worryingly we find that TWAS gets the sign wrong around 1/3 of the time (compared to 50% for pure guessing). You can read more about our analysis here, and what we think is going on 👇

Nikhil Milind@nikhilmilind.dev

How well does TWAS estimate a gene’s direction of effect on a trait? We think of this as an important stress-test for the accuracy of TWAS. In a new pre-print, we find that TWAS gets the sign wrong around 20-30% of the time! doi.org/10.64898/202... 1/n

Jeffrey Pullin reposted

How well does TWAS estimate a gene’s direction of effect on a trait? We think of this as an important stress-test for the accuracy of TWAS. In a new pre-print, we find that TWAS gets the sign wrong around 20-30% of the time! doi.org/10.64898/202... 1/n

doi.orgHigh false sign rates in transcriptome-wide association studiesTranscriptome-wide association studies (TWAS) are widely used to identify genes involved in complex traits and to infer the direction of gene effects on traits. However, despite their popularity, it r...

Jeffrey Pullin reposted

Jeffrey Pullin reposted

Jeffrey Pullin reposted

First time on Bsky and first big announcement! I am excited to announce that our new study explaining the missing heritability of many phenotypes using WGS data from ~347,000 UK Biobank participants has just been published in @Nature. Our manuscript is here: www.nature.com/articles/s41....

nature.comEstimation and mapping of the missing heritability of human phenotypes - NatureWGS data were used from 347,630 individuals with European ancestry in the UK Biobank to obtain high-precision estimates of coding and non-coding rare variant heritability for 34 co...

Jeffrey Pullin reposted

Jeffrey Pullin reposted

Jeffrey Pullin reposted

Jeffrey Pullin reposted

I feel incredibly privileged to share this study on Fanconi anaemia, based on a small but important cohort. This work describes the genetics and clinical outcomes of patients in Australia and New Zealand with a diagnosis of FA. www.sciencedirect.com/science/arti...

sciencedirect.comClinical and genetic spectrum of Fanconi anemia in Australia and New ZealandFanconi anemia (FA) is a rare genetic condition that predisposes to progressive bone marrow failure, a specific spectrum of malignancies, including he…

Jeffrey Pullin reposted

Jeffrey Pullin reposted

New preprint alert: tinyurl.com/tenk10k-multiome. Excited to share our analysis on the impact of genetic variants on single-cell chromatin accessibility in blood, using scATAC-seq and WGS from over 1,000 donors and 3.5M nuclei as part of TenK10K phase 1 🧬 🧵👇 (1/n)

tinyurl.comGenetic regulation of cell type-specific chromatin accessibility shapes immune function and disease riskUnderstanding how genetic variation influences gene regulation at the single-cell level is crucial for elucidating the mechanisms underlying complex diseases. However, limited large-scale single-cell multi-omics data have constrained our understanding of the regulatory pathways that link variants to cell type-specific gene expression. Here we present chromatin accessibility profiles from 3.5 million peripheral blood mononuclear cells (PBMCs) across 1,042 donors, generated using single-cell ATAC-seq and multiome (RNA+ATAC) sequencing, with matched whole-genome sequencing, generated as part of the TenK10K program. We characterized 440,996 chromatin peaks across 28 immune cell types and mapped 243,273 chromatin accessibility quantitative trait loci (caQTLs), 60% of which are cell type-specific. Integration with TenK10K scRNA-seq data (5.4 million PBMCs) identified 31,688 candidate cis-regulatory elements colocalized with eQTLs; over half (52.5%) show evidence of causal effects mediated via chromatin accessibility. Integrating caQTLs with GWAS summary statistics for 16 diseases and 44 blood traits uncovered 9.8% - 30.0% more colocalized signals compared with using eQTLs alone, many of which have not been reported in prior studies. We demonstrate cell type-specific mechanisms, such as a regulatory effect on IRGM acting through altered promoter chromatin accessibility in CD8 effector memory T cells but not in naive cells. Using a graph neural network, we inferred peak-to-gene relationships from unpaired multiome data by incorporating caQTL and eQTL signals, achieving up to 80% higher accuracy compared to using paired multiome data without QTL information. This improvement further enhanced gene regulatory network inference, leading to the identification of 128 additional transcription factor (TF)-target gene pairs (a 22% increase). These findings provide an unprecedented single-cell map of chromatin accessibility and genetic variation in human circulating immune cells, establishing a powerful resource for dissecting cell type-specific regulation and advancing our understanding of genetic risk for complex diseases. ### Competing Interest Statement L.C., E.B.D., and K.K.H.F. are employed at Illumina Inc. D.G.M. is a paid advisor to Insitro and GSK, and receives research funding from Google and Microsoft, unrelated to the work described in this manuscript. G.A.F reports grants from National Health and Medical Research Council (Australia), grants from Abbott Diagnostic, Sanofi, Janssen Pharmaceuticals, and NSW Health. G.A.F reports honorarium from CSL, CPC Clinical Research, Sanofi, Boehringer-Ingelheim, Heart Foundation, and Abbott. G.A.F serves as Board Director for the Australian Cardiovascular Alliance (past President), Executive Committee Member for CPC Clinical Research, Founding Director and CMO for Prokardia and Kardiomics, and Executive Committee member for the CAD Frontiers A2D2 Consortium. In addition, G.A.F serves as CMO for the non-profit, CAD Frontiers, with industry partners including, Novartis, Amgen, Siemens Healthineers, ELUCID, Foresite Labs LLC, HeartFlow, Canon, Cleerly, Caristo, Genentech, Artyra, and Bitterroot Bio, Novo Nordisk and Allelica. In addition, G.A.F has the following patents: "Patent Biomarkers and Oxidative Stress" awarded USA May 2017 (US9638699B2) issued to Northern Sydney Local Health District, "Use of P2X7R antagonists in cardiovascular disease" PCT/AU2018/050905 licensed to Prokardia, "Methods for treatment and prevention of vascular disease" PCT/AU2015/000548 issued to The University of Sydney/Northern Sydney Local Health District, "Methods for predicting coronary artery disease" AU202290266 issued to The University of Sydney, and the patent "Novel P2X7 Receptor Antagonists" PCT/AU2022/051400 (23.11.2022), International App No: WO/2023/092175 (01.06.2023), issued to The University of Sydney. ### Funding Statement A.X. is supported by NHMRC Investigator grant 2033018. J.E.P. is supported by NHMRC Investigator grant 2034556, and a Fok Family Fellowship; D.G.M. is supported by an NHMRC investigator grant (2009982). G.A.F. and the BioHEART Study have been supported by NHMRC Investigator Grant, NSW Health Office of Health and Medical Research, and the NSW Health Statewide Biobank scheme. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The Human Research Ethics Committee of St Vincent's Hospital gave ethical approval for this work. The National Statement on Ethical Conduct in Human Research of the National Health and Medical Research Council gave ethical approval for this work. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Raw caQTL summary statistics will be available at Zenodo website prior to acceptance. [https://github.com/powellgenomicslab/tenk10k\_phase1\_multiome][1] [1]: https://github.com/powellgenomicslab/tenk10k_phase1_multiome

Jeffrey Pullin reposted

Jeffrey Pullin reposted

Jeffrey Pullin reposted

Jeffrey Pullin reposted

Jeffrey Pullin reposted

🔔Paper alert! Extremely excited to share a preprint from our lab! Spearheaded by @axel-schmidt.bsky.social, a super talented medical & computational geneticist, we studied latent Epstein-Barr virus (EBV) infection at population-scale. Interested in how this works & what we found? Read along! 👇

medRxivpreprint@medrxivpreprint.bsky.social

Host control of latent Epstein-Barr virus infection https://www.medrxiv.org/content/10.1101/2025.07.19.25331823v1

Jeffrey Pullin reposted

Super excited to see this out. What started as some math in a grant in 2020, to a student deciding to take this on in 2022, to published in 2025. These things can take time and patience is key!

Nature Genetics@natgenet.nature.com

📢OUT TODAY @natgenet.nature.com 📰Improved multiancestry fine-mapping identifies cis-regulatory variants underlying molecular traits and disease risk. By @zeyunlu.bsky.social, @nmancuso.bsky.social and colleagues. ⬇️ www.nature.com/articles/s41...