1
1. Extended Data 1
Figure # Figure title
One sentence only
Filename
This should be
the name the file
is saved as when
it is uploaded to
our system.
Please include
the file
extension. i.e.:
Smith_ED
Fig1.jpg
Figure Legend
If you are citing a reference for the first time in
these legends, please include all new
references in the Online Methods References
section, and carry on the numbering from the
main References section of the paper.
Extended Data
Fig. 1
Study design
Extended Data
Fig.1. Study
design.tif
We applied the multi-trait analysis of GWAS
(MTAG) algorithm to datasets of European
descent (unless otherwise specified). a, We
applied MTAG to four datasets (glaucoma case-
control GWAS from the UKBB; GWAS meta-
analysis of intraocular pressure (IOP) from the
International Glaucoma Genetics Consortium
(IGGC) and the UKBB; Vertical cup-disc ratio
(VCDR) GWAS data that was either adjusted for
vertical disc diameter (VDD) in the UKBB
dataset; or not adjusted for VDD in the IGGC).
Novel variants identified through this analysis
were then confirmed in two independent data
sets: an Australasian cohort of advanced
glaucoma (ANZRAG) and a consortium of
cohorts from the United States
(NEIGHBORHOOD). The clinical significance of
the PRS derived from the MTAG analysis was
validated in independent samples: first, in
advanced glaucoma cases (ANZRAG and
samples from Southampton/Liverpool in the
UK), and second, in a prospectively monitored
clinical cohort with early manifest glaucoma
(PROGRESSA). b, Prediction in BMES, where
we removed the IGGC VCDR and IGGC IOP
GWAS from the training datasets, given that
they contain BMES data. c, Prediction in the
UKBB glaucoma and ICD-10 POAG cases. Here
we removed all glaucoma cases and 3,000
controls with IOP/VCDR measurements as well
as their relatives from UKBB VCDR/IOP GWAS.
We also evaluated the performance of PRS in
non-European ancestry (192 cases and 6,841
controls of South Asian ancestry in UKBB). d,
Cumulative risk of glaucoma in UKBB. For the
analysis of MYOC p.Gln368Ter carriers (n =
965; cases = 72; controls = 893), participants
were stratified into tertiles of PRS. We also
examined cumulative risk of glaucoma in the
general population (i.e. in MYOC p.Gln368Ter
non-carriers, n = 381,196; cases = 7,381;
controls = 373,815) stratifying by deciles of the
PRS. The discovery and testing datasets were
designed to derive the PRS with no sample
overlap (Supplementary Note).
2
2. Supplementary Information: 3
4
2
A. Flat Files 5
Item Present? Filename
This should be the
name the file is
saved as when it is
uploaded to our
system, and
should include the
file extension. The
extension must
be .pdf
A brief, numerical description of file
contents.
i.e.: Supplementary Figures 1-4,
Supplementary Note, and Supplementary
Tables 1-4.
Supplementary
Information
Yes NG_format_glau
coma_multitrait_
SuppAppendix_
merge
Supplementary Note, Supplementary
Figures 1-13 and Supplementary Tables 1-
13
Reporting Summary
Yes
6
7
8
Multitrait analysis of glaucoma identifies new risk loci and enables polygenic prediction of 9
disease susceptibility and progression 10
11
Jamie E. Craig
1,40
, Xikun Han
2,3,40
*, Ayub Qassim
1,40
, Mark Hassall
1
, Jessica N. Cooke Bailey
4
, Tyler 12
G. Kinzy
4
, Anthony P. Khawaja
5
, Jiyuan An
2
, Henry Marshall
1
, Puya Gharahkhani
2
, Robert P. Igo Jr.
4
, 13
Stuart L. Graham
6
, Paul R. Healey
7,8
, Jue-Sheng Ong
2
, Tiger Zhou
1
, Owen Siggs
1
, Matthew H. Law
2
, 14
Emmanuelle Souzeau
1
, Bronwyn Sheldrick
1
, Pirro G. Hysi
9
, Kathryn P. Burdon
10
, Richard A. Mills
1
, 15
John Landers
1
, Jonathan B. Ruddle
11
, Ashish Agar
12
, Anna Galanopoulos
13
, Andrew J. R. White
7
, 16
Colin E. Willoughby
14,15
, Nicholas Andrew
1
, Stephen Best
16
, Andrea L. Vincent
17
, Ivan Goldberg
18
, 17
Graham Radford-Smith
2
, Nicholas G. Martin
2
, Grant W. Montgomery
19
, Veronique Vitart
20
, Rene 18
Hoehn
21
, Robert Wojciechowski
22,23
, Jost B. Jonas
24
, Tin Aung
25
, Louis R. Pasquale
26
, Angela Jane 19
Cree
27
, Sobha Sivaprasad
28
, Neeru A. Vallabh
29,30
, NEIGHBORHOOD consortium
31
, UK Biobank Eye 20
and Vision Consortium
31
, Ananth C. Viswanathan
5
, Francesca Pasutto
32
, Jonathan L. Haines
4
, 21
Caroline C. W. Klaver
33
, Cornelia M. van Duijn
34
, Robert J. Casson
35
, Paul J. Foster
5
, Peng Tee 22
Khaw
5
, Christopher J. Hammond
9
, David A. Mackey
10,36
, Paul Mitchell
37
, Andrew J. Lotery
38
, Janey L. 23
Wiggs
39
, Alex W. Hewitt
10,40
and Stuart MacGregor
2,40
24
25
1. Department of Ophthalmology, Flinders University, Flinders Medical Centre, Bedford Park, 26
Australia. 27
2. QIMR Berghofer Medical Research Institute, Brisbane, Australia. 28
3. School of Medicine, University of Queensland, Brisbane, Australia. 29
4. Department of Population and Quantitative Health Sciences, Institute for Computational 30
Biology, Case Western Reserve University School of Medicine, Cleveland, OH, USA. 31
5. NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL 32
Institute of Ophthalmology, London, UK. 33
6. Faculty of Medicine and Health Sciences, Macquarie University, Sydney, Australia. 34
7. Centre for Vision Research, Westmead Institute for Medical Research, University of Sydney, 35
3
Sydney, Australia. 36
8. Clinical Ophthalmology & Eye Health, Westmead Clinical School, University of Sydney, 37
Sydney, Australia. 38
9. Department of Ophthalmology, King’s College London, St. Thomas’ Hospital, London, UK. 39
10. Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia. 40
11. Centre for Eye Research Australia, University of Melbourne, Melbourne, Australia. 41
12. Department of Ophthalmology, Prince of Wales Hospital, Randwick, New South Wales, 42
Australia. 43
13. South Australian Institute of Ophthalmology, Royal Adelaide Hospital, Adelaide, South 44
Australia, Australia. 45
14. Biomedical Sciences Research Institute, Ulster University, Coleraine, Northern Ireland, UK. 46
15. Royal Victoria Hospital, Belfast Health and Social Care Trust, Belfast, Northern Ireland, UK. 47
16. Eye Department, Greenlane Clinical Centre, Auckland District Health Board, Auckland, New 48
Zealand. 49
17. Department of Ophthalmology, University of Auckland, Auckland, New Zealand. 50
18. Discipline of Ophthalmology, University of Sydney, Sydney Eye Hospital, Sydney, Australia. 51
19. Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia. 52
20. MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, University of 53
Edinburgh, Edinburgh, UK. 54
21. Department of Ophthalmology, University Hospital Bern, Inselspital, University of Bern, Bern, 55
Switzerland. 56
22. Department of Epidemiology and Medicine, Johns Hopkins Bloomberg School of Public 57
Health, Baltimore, MD, USA. 58
23. Computational and Statistical Genomics Branch, National Human Genome Research 59
Institute, National Institutes of Health, Bethesda, MD, USA. 60
24. Department of Ophthalmology, Medical Faculty Mannheim of the Ruprecht-Karls-University of 61
Heidelberg, Mannheim, Germany. 62
25. Singapore Eye Research Institute, Singapore National Eye Centre, Singapore. 63
26. Icahn School of Medicine at Mount Sinai, New York, NY, USA. 64
27. Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, 65
Southampton, UK. 66
28. NIHR Moorfields Biomedical Research Centre, London, UK. 67
29. Department of Eye and Vision Science, Institute of Ageing and Chronic Disease, University of 68
Liverpool, Liverpool, UK. 69
30. St Paul’s Eye Unit, Royal Liverpool University Hospital, Liverpool, UK. 70
31. The individual members of this consortium are listed in the Supplementary Note. 71
32. Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, 72
Germany. 73
33. Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands. 74
34. Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands. 75
4
35. South Australian Institute of Ophthalmology, University of Adelaide, Adelaide, South Australia, 76
Australia. 77
36. Lions Eye Institute, Centre for Vision Sciences, University of Western Australia, Nedlands, 78
Australia. 79
37. Department of Ophthalmology and Westmead Institute for Medical Research, University of 80
Sydney, Sydney, Australia. 81
38. Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, 82
Southampton, UK. 83
39. Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear 84
Infirmary, Boston, MA, USA. 85
40. These authors contributed equally. 86
87
*E-mail: Xikun.Han@qimrberghofer.edu.au 88
89
Glaucoma, a disease characterized by progressive optic nerve degeneration, can be prevented 90
through timely diagnosis and treatment. We characterized optic nerve photographs of 67,040 91
UK Biobank participants and used a multitrait genetic model to identify risk loci for glaucoma. 92
A novel glaucoma polygenic risk score (PRS) enables effective risk stratification in unselected 93
glaucoma cases, and modifies penetrance of MYOC p.Gln368Ter, the most common glaucoma-94
associated myocilin variant. In the unselected glaucoma population, individuals in the top PRS 95
decile reach an absolute risk for glaucoma 10 years earlier than the bottom decile, and are at 96
15-fold increased risk of developing advanced glaucoma (top 10% vs. remaining 90% OR = 97
4.20). The PRS predicts glaucoma progression in prospectively monitored early manifest 98
glaucoma cases (P = 0.004), and surgical intervention in advanced disease (P = 3.6 × 10
-6
). This 99
glaucoma PRS will facilitate the development of a personalized approach for earlier treatment 100
of high-risk individuals, with less intensive monitoring and treatment possible for lower-risk 101
groups. 102
103
Glaucoma refers to a group of ocular conditions united by a clinically characteristic optic neuropathy 104
associated with, but not dependent on, elevated intraocular pressure
1
. It is the leading cause of 105
irreversible blindness worldwide and is predicted to affect 76 million by 2020
2,3
. There is no single 106
definitive biomarker for glaucoma, and diagnosis involves assessing clinical features, with 107
characterization of the optic nerve head carrying the strongest evidential weight. Primary open-angle 108
glaucoma (POAG) is the most prevalent subtype of glaucoma in people of European and African 109
5
ancestry
2,4
. POAG is asymptomatic in the early stages, and currently approximately half of all cases in 110
the community are undiagnosed even in developed countries
5
. Early detection is paramount as 111
existing treatments are unable to restore vision that has been lost, and late presentation is a major 112
risk factor for blindness
6
. Thus, better strategies to identify high-risk individuals are urgently needed
7
, 113
and more refined approaches can capitalize on the fact that POAG is one of the most heritable of all 114
common human diseases
8–10
. The lack of a currently cost-effective screening strategy for glaucoma
7
, 115
coupled with very high heritability, make glaucoma an ideal candidate disease for the development 116
and application of a polygenic risk score to facilitate risk stratification. 117
Overlap of features shared by healthy optic nerves with those in early stages of glaucoma 118
makes it a difficult disease to diagnose early, necessitating costly ongoing monitoring of patients for 119
progressive optic nerve degeneration
1
. Once a glaucoma diagnosis is established, rates of 120
progression vary widely between individuals, and considerable time can elapse before surveillance 121
techniques adequately differentiate slow from more rapidly progressing cases
1
. Progressive vision 122
loss from glaucoma can be slowed, or in some cases halted, by timely intervention to reduce 123
intraocular pressure using medical therapy, laser trabeculoplasty or incisional surgery
1
. The ability to 124
predict progression is currently crude, with delays in treatment escalation for high-risk individuals an 125
important and inevitable consequence, as well as substantial cost and morbidity associated with 126
overtreatment of lower risk cases. 127
The chronicity, heritability, clinical heterogeneity and treatability of POAG make it an ideal 128
candidate for genetic risk profiling
11,12
. In this study, we evaluated the optic nerve head in 67,040 UK 129
Biobank participants (UKBB), enabling the largest genome-wide association study (GWAS) on optic 130
nerve morphology to date, using vertical cup-disc ratio (VCDR) as an endophenotype for glaucoma. 131
We then incorporated additional genetic data from a second well established glaucoma 132
endophenotype, intraocular pressure (IOP), and combined this with glaucoma disease status using a 133
recently developed multiple trait analysis of GWAS (MTAG)
13
approach to first identify new risk loci for 134
glaucoma, and then generate a comprehensive glaucoma polygenic risk score (PRS). We examined 135
the impact of newly implicated glaucoma genes in independent case-control cohorts from Australia, 136
the United States, and the United Kingdom, and then evaluated the utility of the PRS for predicting 137
glaucoma risk, and important clinical outcomes in well-characterized cases across a range of disease 138
severities. 139