Autoencoder-based phenotyping of ophthalmic images highlights genetic loci influencing retinal morphology and provides informative biomarkers

Sergouniotis, Panagiotis I
Diakite, Adam
Gaurav, Kumar
Allen, Naomi
Aslam, Tariq
Atan, Denize
Barman, Sarah
Barrett, Jenny
Bishop, Paul
Black, Graeme
Braithwaite, Tasanee
Carare, Roxana
Chakravarthy, Usha
Chan, Michelle
Chua, Sharon
Day, Alexander
Desai, Parul
Dhillon, Bal
Dick, Andrew
Doney, Alexander
Egan, Cathy
Ennis, Sarah
Foster, Paul
Fruttiger, Marcus
Gallacher, John
Garway-Heath, David
Gibson, Jane
Guggenheim, Jeremy
Hammond, Chris
Hardcastle, Alison
Harding, Simon
Hogg, Ruth
Hysi, Pirro
Keane, Pearse
Khaw, Peng Tee
Khawaja, Anthony
Lascaratos, Gerassimos
Littlejohns, Thomas
Lotery, Andrew
Luben, Robert
Luthert, Phil
Macgillivray, Tom
Mackie, Sarah
Madhusudhan, Savita
Mcguinness, Bernadette
Mckay, Gareth
Mckibbin, Martin
Moore, Tony
Morgan, James
O’Sullivan, Eoin
Oram, Richard
Owen, Chris
Patel, Praveen
Paterson, Euan
Peto, Tunde
Petzold, Axel
Pontikos, Nikolas
Rahi, Jugnoo
Rudnicka, Alicja
Sattar, Naveed
Self, Jay
Sergouniotis, Panagiotis
Sivaprasad, Sobha
Steel, David
Stratton, Irene
Strouthidis, Nicholas
Sudlow, Cathie
Sun, Zihan
Tapp, Robyn
Thomas, Dhanes
Trucco, Emanuele
Tufail, Adnan
Viswanathan, Ananth
Vitart, Veronique
Weedon, Mike
Williams, Cathy
Williams, Katie
Woodside, Jayne
Yates, Max
Yip, Jennifer
Zheng, Yalin
Birney, Ewan
Fitzgerald, Tomas

European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, United Kingdom
Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9NT, United Kingdom
Manchester Centre for Genomic Medicine, Saint Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester M13 9WL, United Kingdom
Manchester Royal Eye Hospital, Manchester University NHS Foundation Trust, Manchester M13 9WL, United Kingdom
European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, United Kingdom
European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, United Kingdom
European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, United Kingdom
European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, United Kingdom

Corresponding authors. Panagiotis I. Sergouniotis, Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Oxford Road, Manchester M13 9WL, United Kingdom. E-mail: [email protected]; Tomas Fitzgerald, EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom. E-mail: [email protected].

Received June 17, 2024

Received in revised form October 08, 2024

Accepted December 11, 2024

Revised January 21, 2025

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

Bioinformatics 41(1), January 2025. | DOI: 10.1093/bioinformatics/btae732