Genomic Insights for Personalized Care: Motivating At-Risk Individuals Toward Evidence-Based Health Practices medrxiv.org/cgi/content/sh… #medRxiv

Our new paper on semi-supervised machine learning method for predicting homogeneous ancestry groups to assess HWE in diverse whole #genome sequencing studies. The work was motivated by NHGRI Genome Sequencing Program - CCDG data. Applied to HWE QC of 60,000+ diverse whole genomes

Excited to have you Aoxing Liu , really looking forward to your talk!!

Excited to share our preprint for SPLENDID, a new PRS method using continuous ancestry interactions and biobank-scale individual level data. Many thanks to Haoyu Zhang , Rahul Mazumder, and Xihong Lin for their valuable guidance on this work! biorxiv.org/content/10.110…

SPLENDID uses an ensemble group-L0L2 penalized regression framework to model interactions between genetic variants and ancestry PCs. This allows for simultaneous estimation of shared and heterogeneous effects across diverse populations without discrete ancestry labels.

Using training data from All of Us and validation in UK Biobank, SPLENDID outperforms existing methods, particularly in non-European ancestry, selects fewer variants, remains robust to ancestry proportions in tuning, and can be used with only training data.

SPLENDID enables computation of a single, label-free model with robust prediction across all ancestries, which we hope can enhance fairness and interpretability in clinical implementation. Software and tutorials are available on GitHub. github.com/chen-tony/SPLE…

Just in time, I'll be presenting this work today at the HarvardPQG conference in Boston, and at the ASHG conference in Denver. Looking forward to comments, feedback, and discussion!

Check out the presentations from our lab and our close collaborators #ASHG2024. Such a hard-working year. So proud of the group!!! Very humbled to be able to work with so many great collaborators Xihao Li Xihong Lin Pete Kraft Diptavo Dutta Hongyu Zhao Tony Julie Alexia

🚀 Excited to share our new preprint on RICE, a PRS framework that integrates common and rare variants to enhance genetic risk prediction across diverse ancestries! Led by my postdoc fellow Jacob Williams, co-mentored with Xihao Li. Check it out here: medrxiv.org/content/10.110… 1/N

Our paper introducing a PRS-based translation roadmap for lung cancer care is now published on eBioMedicine – The Lancet Discovery Science ! Wonderful collaboration with Haoyu Zhang , Li-Shiun Chen , ILCCO and GSCAN towards the clinical implementation of PRS. sciencedirect.com/science/articl…

Just in time! Come join us with Saori Sakaue on 11/19 for her recent work revealing genetic regulatory mechanisms through eQTL causal variants! Harvard Biostatistics Harvard Epidemiology

Please join us for our last HarvardPQG Working Group seminar of 2024, next Tuesday with Yosuke Tanigawa presenting his exciting recent work on polygenic prediction!

📢Out now! Xihao Li, Pradeep Natarajan, Zilin Li, Zhonghua Liu, Xihong Lin, and colleagues from NIH NHLBI present a framework for functionally-informed multi-trait rare variant analysis of biobank-scale sequencing studies. nature.com/articles/s4358… 🔓rdcu.be/d82Fx

Please join us tomorrow at HSPH for a HarvardPQG Working Group seminar with Kun-Hsing Yu , who will be discussing AI foundation models in pathology!

Excited to share our new manuscript on evaluating multi-ancestry GWAS methods using large-scale simulations & real data from UK Biobank (N≈324K) & All of Us (N≈207K)! My first thesis paper under the guidance of Pete Kraft & Haoyu Zhang. Available at: medrxiv.org/content/10.110…