Scientist Stories: Christoph Lippert, Unleashing the Genetic Architecture of Heritable Traits

30 Dec 2023 · 1 min
0:35

In this Data Science Seminar, Prof. Christoph Lippert presents his research on using machine learning, especially deep learning, together with statistical genetics to uncover the genetic architecture of complex, heritable traits. He begins with a concise overview of genome‑wide association studies (GWAS) and polygenic risk scores (PRS), illustrating how large‑scale GWAS meta‑analyses have identified thousands of SNP‑trait associations but individual effect sizes are small. Lippert explains how the INTERVEEEN consortium aggregates European biobank data (~2 million individuals) to compute PRS that can stratify disease risk (e.g., type‑2 diabetes) and guide public‑health screening. He then shifts to the challenge of high‑dimensional phenotypes such as MRI or retinal fundus images, where traditional GWAS would require compressing images to a single scalar. Lippert proposes a “transfer‑GWAS” pipeline: (1) use a pretrained convolutional neural network (CNN) to extract hidden‑layer embeddings from images, (2) optionally reduce dimensionality with PCA, and (3) perform GWAS on these embeddings using a kernel‑based two‑sample test (maximum‑mean‑discrepancy) or a linear model that incorporates covariates. He discusses two strategies for obtaining the CNN: (a) sample‑split training on the same cohort, which sacrifices test sample size, and (b) transfer learning from large external image datasets (ImageNet or a retinal‑specific Kaggle set). Empirical results on UK Biobank retinal images show many genome loci associated with image variation, some overlapping known eye‑disease genes, and a trade‑off between number of hits and effect strength depending on the pretraining source. Lippert acknowledges limited interpretability of image‑based associations and outlines ongoing work on explainable AI methods (collaboration with Wojciech Samek) and theoretical extensions (with Sonja Greven). The talk concludes with a description of rare‑variant set tests developed by his student Remo: (1) aggregate ultra‑rare variants into functional sets, (2) construct kernels weighted by neural‑network‑predicted functional annotations, (3) use a small‑permutation‑plus‑parametric‑fit approach to obtain accurate p‑values at GWAS scale. This method improves power and interpretability, exemplified by a discovered missense variant in PIEZO1 affecting red‑blood‑cell biomarkers. Overall, Lippert’s work demonstrates how deep learning can be fused with rigorous statistical testing to leverage massive, high‑dimensional biomedical data for genetic discovery and potential clinical translation.

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