Population Structure Analysis of an Inbred Population using Quantitative Shape Phenotyping from Stereo Retinal Photographs

Abstract:The population structure of an inbred population of 781 people on Norfolk Island in the Pacific, 318 of which are descendants of the original Mutineers of the Bounty, is analyzed phenotypically using shape from stereo retinal fundus photographs. Three-dimensional optic nerve head (ONH) shape is reconstructed from stereo pairs by a multi-scale stereo matching algorithm. Using deep neural network, the shape of ONH, which is under genetic control, is decomposed into a set of hierarchical features through self-taught learning. Features captured at different levels are selected according to their discriminant power in identifying the two populations. The prediction accuracy is evaluated with stratified cross validation. Given the selected feature set, individuals are grouped into k hierarchical clusters and cluster membership fractions are determined for k=2,3,4,5,6,7. Population structure analysis on the basis of phenotypes through image analysis allows heritability and linkage analysis, including founder effects from English and Polynesian ancestors, potentially leading to new genetic risk factors for glaucoma and other ONH-related eye diseases.

Machine Learning (cs.LG); Computer Vision and Pattern Recognition (cs.CV); Quantitative Methods (q-bio.QM)

arXiv:2608.15471 [cs.LG]

(or arXiv:2608.15471v1 [cs.LG] for this version)

https://doi.org/10.48550/arXiv.2608.15471 Focus to learn more arXiv-issued DOI via DataCite (pending registration)

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