ARTICLE
Recei ed 9 Feb 2015 |Accep ed 10 Feb 2016 |Published 6 Ap 2016
Me a-analysis o gene–en i onmen -wide
associa ion scans accoun ing o educa ion le el
iden ifies addi ional loci o e ac i e e o
Qiao Fan e al.#
Myopia is he mos common human eye diso de and i esul s om complex gene ic and
en i onmen al causes. The apidly inc easing p e alence o myopia poses a majo public
heal h challenge. He e, he CREAM conso ium pe o ms a join me a-analysis o es single-
nucleo ide polymo phism (SNP) main e ec s and SNP educa ion in e ac ion e ec s on
e ac i e e o in 40,036 adul s om 25 s udies o Eu opean ances y and 10,315 adul s om
9 s udies o Asian ances y. In Eu opean ances y indi iduals, we iden i y six no el loci
(FAM150B-ACP1,LINC00340,FBN1,DIS3L-MAP2K1,ARID2-SNAT1 and SLC14A2) associa ed
wi h e ac i e e o . In Asian popula ions, h ee genome-wide significan loci AREG,GABRR1
and PDE10A also exhibi s ong in e ac ions wi h educa ion (Po8.5 105), whe eas he
in e ac ions a e less e iden in Eu opeans. The disco e y o hese loci ep esen s an
impo an ad ance in unde s anding how gene and en i onmen in e ac ions con ibu e o he
he e ogenei y o myopia.
Co espondence and eques s o ma e ials should be add essed o C.C.W.K (email: c.c.w[email p o ec ed]) o o S.-M.S.
(email: [email protected]). #A ull lis o au ho s and hei a filia ions appea s a he end o he pape .
DOI: 10.1038/ncomms11008 OPEN
NATURE COMMUNICATIONS | 7:11008 | DOI: 10.1038/ncomms11008 | www.na u e.com/na u ecommunica ions 1
Myopia, o nea sigh edness, has apidly eme ged as a
global heal h conce n in he las h ee decades1.I is
one o he leading causes o isual impai men and
is associa ed wi h po en ially blinding ocula complica ions
including myopic maculopa hy, glaucoma, ca a ac and e inal
de achmen 2. E idence om amily and win s udies s ongly
suppo s he he i abili y o myopia3. Es ima es o he he i abili y
o he quan i a i e ai e ac i e e o ha e been epo ed o be
as high as 90% ( e . 4). On he o he hand, he apid upsu ge o
myopia in he las ew decades in many pa s o he wo ld is likely
o be a consequence o li es yle changes such as he inc easing
educa ional in ensi y, in pa icula in u ban Eas Asia5,6, and
po en ially gene and en i onmen (G E) in e ac ions.
Majo a emp s unde aken in genome-wide associa ion s udies
(GWAS) o elucida e he gene ic de e mina ion o myopia and
e ac i e e o ha e ecen ly led o he disco e y o 430
dis inc suscep ibili y loci7,8. Ne e heless, collec i ely hese
gene ic a ian s a e es ima ed o explain o12% o pheno ypic
a iance in e ac i e e o 7,8. As myopia is a esul o he
combina ion o gene ic and en i onmen al ac o s, in e play
be ween genes and en i onmen may accoun o a subs an ial
p opo ion o he pheno ypic a iance. In ecen imes, we
showed in e ac ions be ween educa ion and gene ic isk sco e o
myopia de i ed om 26 known GWAS single-nucleo ide
polymo phisms (SNPs) in he Ro e dam S udy9; he combined
e ec o gene ic p edisposi ion and educa ion on he isk o
myopia was subs an ially g ea e han an icipa ed om a simple
sum o hese wo ac o s. A he gene le el, some genes such as
SHISA6-DNAH9 ha e been shown o in e ac wi h educa ion
le el and exhibi s ong gene ic e ec s o myopia among Asians
wi h a leas highe seconda y educa ion10. In he cu en s udy,
we demons a e ha new gene ic e ec s implica ed in myopia
de elopmen could be unco e ed by s udying in e ac ions
be ween gene ic a ian s and educa ion le el.
In he con ex o he ae iology o e ac i e e o s, educa ion
a ainmen is gene ally conside ed a su oga e measu e o
accumula ed nea wo k ac i i y1. When iewing nea objec s, he
eye gene a es ex a op ical powe h ough he p ocess
o accommoda ion o ocus he image on he e inal plane,
o main ain clea ision11. The e is an accommoda i e lag
(less accommoda ion p oduced han needed) in many myopes,
esul ing in a hype opic de ocus on he e ina o nea wo k, which
has long been p oposed o p omo e eye g ow h1,12, bu whe he
his occu s be o e o a e he onse o myopia in humans is less
clea . The e ina has a cen al ole in he mechanism linking such
isual inpu wi h eye g ow h and e ac i e de elopmen 13.Se e al
neu o ansmi e s o molecules ha e been implica ed in his
p ocess by animal s udies including dopamine, ace ylcholine,
asoac i e in es inal pep ide, GABA (g-aminobu y ic acid) and
glucagon14,15. Howe e , an o ganized amewo k o he e inal
signalling mechanisms unde lying e ac i e e o de elopmen
unde a ious en i onmen al condi ions emains o be elucida ed.
Fac o ing in en i onmen al exposu es may enhance powe o
he de ec ion o genes, especially in ci cums ances whe e a gene ic
locus has a di e en ial e ec condi ional on specific en i onmen
exposu es16. Gene–en i onmen -wide in e ac ion s udies (GEWIS)
using a join me a-analysis (JMA) app oach on SNP main e ec s
and SNP en i onmen in e ac ions ha e ecen ly been
desc ibed17,18. This app oach has success ully iden ified six no el
loci associa ed wi h as ing insulin and glucose accoun ing o
in e ac ions wi h body mass index18. I also led o he iden ifica ion
o wo no el loci o pulmona y unc ion ha did no eme ge om
analyses based on he gene ic main e ec s alone19. The well-
documen ed e ec s o educa ional a ainmen on myopia and
e ac i e e o make he p oposed in e ac ion an excellen
analy ical candida e o he GEWIS.
The a ailabili y o la ge-scale GWAS sphe ical equi alen da a
se s om he Conso ium o Re ac i e E o And Myopia
(CREAM) makes G E in e ac ion analyses easible. To iden i y
addi ional gene ic a ian s o e ac i e e o , we pe o med
GEWIS-based analyses on 40,036 adul s o Eu opean ances y
om 25 s udies and 10,315 adul s o Asian ances y om 9
s udies. We iden ified nine new loci using he JMA app oach,
whe e h ee loci exhibi ed G E in e ac ion on e ac i e e o in
Asians, including he GABA
C
ecep o subuni 1 gene GABRR1.
Resul s
Educa ional le el and i s main e ec s on sphe ical equi alen .
The baseline cha ac e is ics o 50,351 pa icipan s om 34 s udies
in ou me a-analysis a e shown in Table 1. A o al o 40,036
pa icipan s we e o Eu opean descen and 10,315 we e o Asian
descen ; he age o he pa icipan s anged om 20 o 99 yea s.
We g ouped indi iduals in o wo educa ional ca ego ies: a highe
educa ion g oup ha included indi iduals who comple ed highe
seconda y o uni e si y educa ion and a lowe educa ion g oup
comp ising hose wi h lowe seconda y educa ion o below
(see Me hods). Among Eu opeans, he p opo ions o pa icipan s
in he highe educa ion g oup anged om 16.5% (FITSA20 and
OGP Talana21) o 94.4% (AREDS22) wi h an a e age o 50.7%
(Supplemen a y Table 1). In Asians, he p opo ions o
indi iduals in he highe educa ion g oup anged om 6.7%
(SiMES23) o 75.9% (Nagahama24) wi h an a e age o 30.0%.
Ac oss all s udies, indi iduals in he highe educa ion g oup had a
sphe ical equi alen e ac i e e o ha was on a e age
0.59 diop es (D) mo e myopic, o less hype opic, compa ed
wi h hose in he lowe educa ion g oup (b¼0.59 D; 95%
confidence in e al (CI): 0.64 o 0.55 D). High educa ion
le el was associa ed wi h a wo old mo e myopic sphe ical
equi alen in indi iduals o Asian as compa ed wi h Eu opean
ances y (Asians: b¼1.09 D, 95% CI: 1.20 o 0.98 D;
Eu opeans: b¼0.49 D, 95% CI: 0.54 o 0.44 D; Fig. 1).
Among Asian s udies, we also obse ed he e ogenei y o
educa ion e ec s o e ac i e e o . The educa ion e ec s on
sphe ical equi alen in Singapo e Chinese we e significan ly
la ge han ha in o he Asian s udies (Singapo e Chinese:
b¼1.75 D, 95% CI: 1.92 o 1.58 D; o he Asian coho s:
b¼0.60 D, 95% CI: 0.75 o 0.46 D).
GEWIS in Eu opeans. A e s ingen quali y con ol (QC)
fil e ing, B6 million SNPs in each s udy we e eligible o he
genome-wide JMA es (Supplemen a y Table 2). The JMA o
SNP main e ec s and SNP educa ion in e ac ions in 40,036
Eu opean Ances y indi iduals showed an associa ion wi h
sphe ical equi alen a 12 p e iously implica ed loci (Fig. 2a,
Supplemen a y Table 3 and Supplemen a y Fig 1). We
also iden ified ou p e iously un epo ed loci associa ed wi h
sphe ical equi alen achie ing genome-wide significance
(P
JMA
o5.0 108;P
he
Z0.086; Table 2): FAM150B-ACP1,
LINC00340,FBN1 and DIS3L-MAP2K1. The significan
associa ion o JMA es ing a hese loci in Eu opeans was
p ima ily d i en by SNP e ec s in bo h he lowe and highe
educa ion s a a (4.40 108 P
main
1.35 106and
7.61 1011 P
main
1.75 106, espec i ely). SNP 
educa ion in e ac ion was no significan (P
in
Z0.208). The es i-
ma ed e ec sizes o SNP e ec s on sphe ical equi alen we e
highly simila ac oss educa ion s a a.
GEWIS in Asians. The JMA o sphe ical equi alen in 10,315
indi iduals om he Asians coho s iden ified genome-wide
significan associa ion o h ee genes: AREG,GABRR1
and PDE10A (P
JMA
o5.0 108; Table 3 and Fig. 2b).
ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms11008
2NATURE COMMUNICATIONS | 7:11008 | DOI: 10.1038/ncomms11008 | www.na u e.com/na u ecommunica ions
SNP educa ion in e ac ion e ec s associa ed wi h sphe ical
equi alen we e obse ed a all h ee loci, wi h gene ic e ec s
significan ly la ge wi hin pa icipan s who had a highe le el o
educa ion compa ed wi h hose wi h a lowe educa ion le el:
AREG ( s12511037, b
in
¼0.89±0.14 D, P
in
¼6.87 1011),
GABRR1 ( s13215566, b
in
¼0.56±0.14 D, P
in
¼8.48 105)
and PDE10A ( s12206610, b
in
¼0.72±0.13 D, P
in
¼2.32
108). The geno ype and pheno ype associa ions we e highly
significan in he highe educa ion s a um (main gene ic e ec s,
1.97 1010 P
main
8.16 108) bu we e conside ably
weake in he lowe educa ion s a um (0.008 P
main
0.243).
The e was no e idence o in e -s udy he e ogenei y a index SNPs
wi hin AREG,GABRR1 o PDE10A loci (Q- es : P
he
Z0.122).
GABRR1 and PDE10A index SNPs we e no associa ed wi h
sphe ical equi alen in Eu opean samples, o ei he he JMA es ,
SNP main e ec o SNP educa ion in e ac ion (Table 3). AREG
SNP s12511037 was excluded in he me a-analysis o Eu opean
s udies a e QC fil e ing; hence, a p oxy SNP, s1246413,
in linkage disequilib ium (LD) wi h s12511037 in Asians
( 2¼0.97) was es ed bu no associa ed wi h sphe ical equi alen
(P
JMA
¼0.527; P
in
¼0.176). The me a- eg ession including
s udy-le el cha ac e is ics as co a ia es in he model confi med
he he e ogenei y be ween popula ions o Eu opean and
Asian ances y (GABRR1:P¼0.006; PDE10A:P¼0.0419;
Supplemen a y Table 4). Fo PDE10A, besides e hnici y, a e age
sphe ical equi alen o each s udy also explained he in e -s udy
he e ogenei y o he in e ac ion e ec s (P¼0.025).
We examined whe he he unde lying assump ion o G E
independence held a hese h ee G E in e ac ion loci. We
pe o med a me a-analysis o logis ic eg ession analysis o
educa ion le el on AREG SNP s12511037, GABRR1 SNP
s13215566 and PDE10A SNP s12296610, adjus ing o age,
gende and popula ion s a ifica ion in Asian coho s
(n¼10,315). Ou analysis did no e eal any significan
associa ions be ween hese loci and educa ion le el (PZ0.102,
P
he
Z0.170; Supplemen a y Table 5). Fu he mo e, he h ee loci
we e no associa ed wi h educa ional a ainmen in a la ge
me a-analysis o GWAS ecen ly conduc ed in Eu opean
coho s25. Thus, ou G E esul s a e unlikely o be biased due
o dependence be ween gene and educa ion.
Table 1 | Cha ac e is ics o s udy pa icipan s.
S udy NS udy yea Age (s.d.) Age ange Male (%) Sphe ical equi alen
Eu opeans (n¼40,036)
ALIENOR 509 2006–2008 79.2 (4.1) 73–93 43.2 0.98 (1.98)
ALSPAC 1,865 1999–2000 45.9 (4.5) 32–59 0 0.76 (2.16)
AREDS 1,842 1992 68.1 (4.7) 55–81 41.0 0.54 (2.15)
BATS 383 1992–2013 24.8 (7.8) 20–67 41.3 0.67 (1.58)
BMES 1,896 1992–2009 66.8 (8.9) 49–94 43.8 0.58 (1.94)
CROATIA-Ko cula 807 2007–2008 56.2 (13.3) 25–94 34.9 0.13 (1.59)
CROATIA-Spli 787 2008–2009 51.9 (13.0) 25–80 38.6 1.27 (1.59)
DCCT 1,057 1982–1993 35.4 (5.8) 25–49 54.1 1.47 (1.80)
EGCUT 904 2002–2013 56 (17.0) 25–99 38.8 0.33 (3.36)
EPIC 1,083 2004–2011 68.8 (7.5) 50–88 43.8 0.34 (2.27)
ERF 2,604 2002–2005 48.9 (14.4) 25–87 45.0 0.12 (2.03)
FES 2,479 1973–1975/ 1989–1991 54.8 (9.3) 28–84 55.3 0.27 (2.37)
FITSA 188 2000–2001 68.5 (3.3) 63–76 0 1.44 (2.08)
GHS1 3,178 2007–2008 55.3 (10.9) 35–74 50.4 0.38 (2.47)
GHS2 1,354 2008 54.6 (10.8) 36–74 49.6 0.39 (2.51)
KORA 2326 2004–2006 55.1 (11.8) 35–84 49.4 0.26 (2.18)
OGP Talana 456 2002 52.6 (16.3) 25–89 57.3 0.20 (0.24)
ORCADES 1,124 2009 56.5 (13.2) 29–92 39.1 0.10 (2.07)
RAINE 348 2010–2012 20.4 (0.34) 20–22 49.1 0.03 (1.29)
RS1 5,702 1991–1993 68.7 (8.7) 55–99 41.0 0.83 (2.55)
RS2 2,021 2000–2002 64.3 (7.9) 55–95 46.0 0.48 (2.51)
RS3 2,918 2006–2009 56.9 (6.6) 45–86 44.0 0.28 (2.60)
TwinsUK 2,154 1998–2010 53.8 (11.4) 25–84 8.4 0.96 (2.78)
WESDR 561 1979–2007 31.7 (7.0) 25–65 50.3 1.65 (2.07)
YFS 1,490 2011 41.9 (5.0) 34–49 44.6 1.09 (2.16)
Asians (n¼10,315)
BES 589 2006–2011 62.1 (8.5) 50–90 34.0 0.06 (1.86)
Nagahama 723 2008–2010 49.2 (15.2) 30–74 33.6 1.93 (2.46)
SCES-610K 1,710 2009–2011 57.5 (7.0) 44–84 51.6 0.72 (2.69)
SCES-OmniE 543 2011–2012 59.3 (8.9) 46–83 51.2 0.89 (2.74)
SiMES 2,256 2004–2006 46.8 (10.2) 40–80 49.1 0.03 (1.81)
SINDI 2,088 2007–2009 55.8 (8.8) 43–84 51.5 0.04 (2.07)
SP2-1M 811 1992–1998 46.8 (10.2) 25–80 62.3 1.80 (2.84)
SP2-610 854 1992–1998 48.4(11.3) 25–82 19.6 1.44 (2.89)
STARS 741 2007–2009 38.5 (5.2) 26–58 52.4 2.80 (2.85)
ALIENOR, an ioxydan s, lipids essen iels, nu i ion e maladies oculaiRes; ALSPAC, a on longi udinal s udy o pa en s and child en; AREDS, age- ela ed eye disease s udy; BATS, B isbane adolescen
wins s udy; BMES, blue moun ains eye s udy; DCCT, diabe es con ol and complica ions ial; EGCUT, es onian genome cen e o he uni e si y o Ta u; EPIC, EPIC-No olk eye s udy; ERF, e asmus
ucphen amily s udy; FES, F amingham eye s udy; FITSA, finnish win s udy on aging; GHS, Gu enbe g heal h s udy; KORA, coope a i e heal h esea ch in he egion o Augsbu g; OGP Talana,
oglias a gene ic pa k, alana s udy; ORCADES, o kney complex disease s udy; RAINE, RAINE eye heal h s udy; RS, Ro e dam s udy; TwinsUK, Twins UK s udy; WESDR, Wisconsin epidemiologic
s udy o diabe ic e inopa hy; YFS, young finns s udy; BES, Beijing eye s udy; SCES, Singapo e Chinese eye s udy; SiMES, Singapo e Malay eye s udy; SINDI, Singapo e Indian eye s udy; SP2, Singapo e
p ospec i e s udy p og am; STARS, s abismus, amblyopia and e ac i e e o s udy in p eschool singapo ean child en. s.d., s anda d de ia ion; age in yea s; sphe ical equi alen in diop es.
De ails o each s udy coho a e desc ibed in Supplemen a y No e 1.
NATURE COMMUNICATIONS | DOI: 10.1038/ncomms11008 ARTICLE
NATURE COMMUNICATIONS | 7:11008 | DOI: 10.1038/ncomms11008 | www.na u e.com/na u ecommunica ions 3
We also e alua ed he associa ion o sphe ical equi alen in
Asian coho s o ou loci iden ified om Eu opean popula ions.
Two o hem showed significan associa ions in he JMA
es : FAM150B-ACP1 (P
JMA
¼0.031) and DIS3L-MAP2K1
(P
JMA
¼0.0042; Table 2). The SNP e ec sizes in lowe and
highe educa ion s a a in Asians we e simila a FAM150B-
ACP1. The signal a he DIS3L-MAP2K1 locus was mainly d i en
by SNP educa ion in e ac ion in Asians (P
in
¼7.95 104),
whe eas he in e ac ion e ec was no s a is ically significan in
Eu opeans (P
in
¼0.208).
Combined GEWIS o all coho s. We subsequen ly conduc ed a
JMA in he combined da a including bo h he Eu opean and
Asian pa icipan s o all 34 s udies. This analysis e ealed wo
addi ional SNPs: ARID2-SNAT1 (P
JMA
¼4.38 108) and
SLC14A2 (P
JMA
¼2.54 108). Bo h loci showed sugges i e
associa ion wi h sphe ical equi alen in Eu opean coho s, wi h
he same di ec ion o e ec and simila e ec sizes in Asian
coho s (Table 2). We also de ec ed genome-wide significan
associa ions wi h sphe ical equi alen o 17 known loci8
iden ified in ou p e ious CREAM GWAS (Supplemen a y
Table 3). The egional plo s o he iden ified no el loci a e
p esen ed in Supplemen a y Fig 2.
Gene and educa ion in e ac ions o GWAS known loci.We
also e alua ed he in e ac ions be ween educa ion and p e iously
epo ed gene ic associa ion wi h sphe ical equi alen a 39 loci
iden ified om ecen wo la ge GWAS s udies7,8. Two
SNP educa ion in e ac ions we e nominally significan
(Supplemen a y Table 6): TJP2 in Eu opeans ( s11145488,
P
in
¼6.91 103) and SHISA6-DNAH9 in Asians ( s2969180,
P
in
¼4.02 103). In gene al, he index SNPs es ed a 39 loci
had la ge SNP educa ion in e ac ion e ec on sphe ical
equi alen in Asians e sus Eu opeans (me a- eg ession P o
old changeso0.001; Supplemen a y Fig. 3). Fo 20 SNPs wi h he
same di ec ion o he in e ac ion e ec , he magni udes o
in e ac ion e ec s we e ou old la ge on a e age in Asians han
in Eu opeans (P¼0.003).
Gene and nea wo k in e ac ions o h ee iden ified loci. High
educa ion le els may eflec an es ima o o he g ea e
accumula i e e ec o nea wo k26,27. We hus examined whe he
he e was e idence o SNP nea wo k in e ac ions associa ed
wi h sphe ical equi alen a he h ee loci (AREG,GABRR1 and
PDE10A) in paedia ic coho s (SCORM28, Guangzhou Twins29
and ALSPAC30; combined n¼5,835; Supplemen a y Table 7).
Ten a i e suppo o a SNP nea wo k in e ac ion was
obse ed o PDE10A ( s12206610, P
in
¼0.032, P
he
¼0.658),
wi h he s onge gene ic e ec in child en spending mo e hou s
on eading, w i ing o compu e use. Weake suppo o an
in e ac ion was no ed a GABRR1 ( s13215566, P
in
¼0.309,
P
he
¼0.655), al hough he di ec ion o me a-analysed in e ac ion
e ec was la gely consis en ac oss paedia ic s udies wi h ha
obse ed in adul s. We did no obse e he in e ac ion a AREG
( s12511037, P
in
¼0.795, P
he
¼0.062).
Gene exp ession in human issues. Using he Ocula Tissue
Da abase31, we examined he exp ession o he associa ed genes in
20 no mal human dono eyes. The majo i y o genes iden ified
we e exp essed in human e ina, scle a, cho oid o e inal
pigmen epi helium (RPE) (Supplemen a y Table 8). Among
hese genes, GABRR1,ACP1 and SNAT1 had he highes
exp ession in he e ina. The P obe Loga i hmic In ensi y
E o -no malized messenge RNA exp ession le els in he
e ina anged om 121.66 o 236.69. O no e, MAP2K1 was
widely exp essed in he e ina, scle a and cho oid/RPE.
 (95% CI) P
All: –0.59 (–0.64, –0.55) <0.0001
Eu opeans: –0.49 (–0.54, –0.44) <0.0001
Asians: –1.09 (–1.20, –0.98) <0.0001
Eu opeans
Asians
-coe icien
–3.0 –2.5 –2.0 –1.5 –1.0 –0.5 0.0 0.5
DCCT
OGP Talana
BMES
CROATIA-Spli
CROATIA-Ko cula
EPIC
BATS
EGCUT
WESDR
ORCADES
RAINE
ALIENOR
FITSA
AREDS
KORA
GHS2
GHS1
RS1
RS2
RS3
Nagahama
BES
SiMES
SlNDI
SP2-610
SP2-1M
STARS
SCES-610K
SCES-OmniE
ERF
YFS
FES
TwinsUK
ALSPAC
Figu e 1 | Fo es plo o educa ion main e ec s on sphe ical equi alen ac oss s udies. The b-coe ficien ep esen s he di e ences o diop es in
e ac i e e o compa ing indi iduals in highe educa ion g oup e sus lowe educa ion g oup in Eu opeans (n¼40,036), Asians ( n¼10,315) and all
s udies (n¼50,351). The s udies a e so ed by e ec size o educa ion on sphe ical equi alen wi hin Eu opeans and Asians s udies, espec i ely.
ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms11008
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Discussion
This s udy ep esen s he mos comp ehensi e genome-wide scan
o gene and educa ion in e ac ions o da e, o e ac i e e o .
He e we iden ified no el gene ic loci associa ed wi h e ac i e
e o by es ing he join con ibu ion o SNP main e ec s and
SNP educa ion e ec s in la ge mul i-e hnic popula ions. Th ee
loci (AREG,GABRR1 and PDE10A) showed s ong in e ac ions
wi h educa ion in popula ions o Asian descen , wi h la ge
gene ic e ec s wi hin pa icipan s who had a highe le el o
educa ion compa ed wi h hose wi h a lowe educa ion le el; no
in e ac ions achie ed s a is ical significance in Eu opeans o op
JMA associa ions o known myopic loci. Apa om confi ming
known associa ions a 17 p e ious published loci, we iden ified six
new loci (FAM150B-ACP1,LINC00340,FBN1,DIS3L-MAP2K1,
ARID2-SNAT1 and SLC14A2) significan ly associa ed wi h
sphe ical equi alen using he combined mul i- acial coho .
A ecen me a-analysis o GWAS in mul i-e hnic popula ions
comp ises 32 s udies (n¼45,756) om CREAM and a la ge
GWAS in Eu opeans (n¼45,771) ha e epo ed a o al o 39
gene ic loci associa ed wi h e ac i e pheno ypes7,8. The cu en
genome-wide me a-analysis included B5,000 mo e subjec s han
he p e ious GWAS o main e ec s. We iden ified nine addi ional
no el loci using he JMA app oach. These loci can be placed
wi hin he biological con ex o he isually e oked signalling
cascade ha begins in he e ina and media es scle a
emodelling32. The newly iden ified genes a e in ol ed in
e inal neu o ansmission (GABRR1 and SNAT1), ex acellula
ma ix emodelling (FBN1,MAP2K1 and AREG), ci cadian
hy hm (PDE10A) and pla ele -de i ed g ow h ac o ecep o
signalling (ACP1) (Supplemen a y Table 9). Ne wo k analysis
e ealed ha mos o he no el genes may end o be co-exp essed
and co-localized wi h he known myopia suscep ibili y genes
h ough mul iple biological ne wo ks such as LAMA2,GJD2,
RASGRF1,BMP3,RDH5,ZMAT4,RBFOX1,RDH5 and so on
(Supplemen a y Fig. 4). Ou da a, in line wi h p e ious findings,
subs an ia e he assump ion o he e ogenei y in he molecula
mechanisms in ol ed in e ac i e e o and myopia.
Among he no el loci, GABRR1 on ch omosome 6q15 (53 kb),
encoding GABA
C
ecep o subuni 1, is an in e es ing unc ional
candida e sugges i e o a ole in myopia de elopmen .
Modula ion o synap ic plas ici y ia GABA-media ed inhibi ion
would be well placed o al e he ‘gain’ o he isually guided
CD55
FAM150B-ACP1
CHRNG
LINC00340
KCNQ5
LAMA2
TOX
TJP2
RDH5
SIX6
GJD2
ARID2
-SNAT1
FBN1
DIS3L-MAP2K1
A2BP1
DNAH9
KCNJ2
SLC14A2
Eu opean ances y popula ions
1 2 3 4 5 6 7 8 9 10 11 12 13 15 16 18 20 221714
20
15
10
5
0
AREG
GABRR1
PDE10A
Asian popula ions
Ch omosome
10
8
6
4
2
0
1234567891011121315161820221714
a
b
–Log10 (P)
–Log10 (P)
Figu e 2 | Manha an plo s o log
10
(P) o he JMA on SNP main e ec s and SNP educa ion e ec s on sphe ical equi alen in (a) Eu opean
ances y popula ions and (b) Asian popula ions. The ho izon al ed line indica es he genome-wide significance le el o P
JMA
o5108. The ho izon al
blue line indica es he sugges i e significance le el o P
JMA
o1105. No el loci eaching genome-wide significance a e labelled in ed and known loci a e
in g ey.
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NATURE COMMUNICATIONS | 7:11008 | DOI: 10.1038/ncomms11008 | www.na u e.com/na u ecommunica ions 5

eedback sys em con olling e ac i e de elopmen 33. The lead SNP
s13215566 in GABRR1, oge he wi h se en SNPs wi hin he LD
block ( 2Z0.8), a e in onic, po en ially a ec ing egula o y mo i s
(such as z p128 and gcm1) ha may influence ansc ip ional
egula ion (Supplemen a y Table 10). The a ian s13215029, in
LD ( 2¼1) wi h s13215566, is associa ed wi h cis-ac ing
exp ession o GABRR1 (P¼2.3 104)inskin issues
(Supplemen a y Table 9)34. A ecen pha macological s udy
p o ided e idence ha e inal dopamine gic and GABAe gic
neu o ansmi e s play a subs an ial ole in he modula ion o
e ac i e de elopmen in o m-dep i a ion myopia35–37.S one
e al.35 ha e epo ed ha an agonis s o GABA-A, -B and -C
ecep o s inhibi ed o m-dep i a ion myopia in chicks, wi h
g ea es e ec in he equa o ial dimension. GABA ecep o s,
exp essed in bipola and ganglion neu on cells, also in e ac wi h
dopamine pa hways in he e ina36. A ecen p o eomics s udy
de e mined ha le els o GABA anspo e -1 we e significan ly
educed in myopic mu ine e ina a e a opine ea men , implying
ha GABA signalling is in ol ed in he an i-myopic e ec s o
a opine37. Al oge he , hese da a sugges ha GABA
C
ecep o 1
may egula e he de elopmen o myopia h ough unc ional
eedback om RPE o neu on cells in he e ina. Fu he s udies a e
needed o in es iga e he e ec o gene ic dele ion o GABRR1 on
e ac i e eye de elopmen and he ole o he GABAe gic pa hway
in myopia de elopmen using gene knockou mice. The e o e, ou
esul in humans is in line wi h animal expe imen s, suppo ing he
no ion ha he GABAe gic neu o ansmi e signalling pa hway in
he e ina could be a po en ial ac o in he p og ession o myopia.
SNP s10889855 on ch omosome 6 is an in onic a ian
wi hin he ARID2 gene (AT- ich in e ac i e domain 2) and
500 kb downs eam o SNAT1 (solu e ca ie amily 38, membe ,
alias SLC38A1). SNAT1 is a anspo e o glu amine, a p ecu so
o GABA38. I is also highly exp essed in human e ina. In ou
p e ious me a-analysis in CREAM8, we iden ified a ian s in
ano he glu ama e ecep o gene GRIA4 (encoding glu ama e
ecep o , iono opic); al oge he , cu en e idence suppo s he
no ion ha e inal neu o ansmi e s GABA and glu amine may
be in ol ed in he e ac i e de elopmen .
The s onges associa ion signal o gene and en i onmen
in e ac ions was om s12511037, loca ed 14 kb downs eam he
AREG gene (amphi egulin). AREG is a ligand o he epide mal
g ow h ac o ecep o p omo ing he g ow h o no mal epi helial
cells, which is c i ical o cell di e en ia ion and p oli e a ion
such as eg ow h o he wounded co nea39. A link has been ound
be ween he musca inic ace ylcholine ecep o s, dominan in
myopia p og ession, and he epide mal g ow h ac o ecep o in
musca inic sys em40,41.
Ano he no el associa ion, s16949788 on ch omosome 15,
de i es om a egion ha spans DIS3L and MAP2K1.MAP2K1
encodes mi ogen-ac i a ed p o ein kinase 1, which binds o
musca inic ecep o s du ing p oli e a ion42 and inhibi s he
p oli e a ion o human scle al fib oblas s exposed o all- ans
e inoic acid43. All- ans e inoic acid is a modula o o ocula
g ow h, inhibi ing he p oli e a ion o human scle al fib oblas s44.
FBN1 (Fib illin 1), a membe o he fib illin amily, encodes a
la ge ex acellula ma ix glycop o ein. Mu a ions in FBN1 cause
Table 2 | Six gene ic loci associa ed wi h sphe ical equi alen om he JMA in he Eu opean popula ions and combined analyses.
SNP (Ch :BP) Gene Allele FREQ Subg oup Eu opeans (n¼40,036) Asians (n¼10,315) All (n¼50,351)
bP- alue P
he
bP- alue P
he
bP- alue P
he
s60843830
(2:286756)
FAM150B-
ACP1
C/G 0.66/0.74 JMA 3.71 10 80.086 0.031 0.980 1.27 1090.395
Lowe
educa ion
0.11 4.73 1080.09 0.010 0.10 1.65 109
Highe
educa ion
0.09 1.75 10 60.06 0.509 0.09 9.83 107
s10946507
(6:22100367)
LINC00340
(6p22.3)
A/G 0.47/0.16 JMA 3.07 1080.213 0.433 0.396 2.24 10 80.249
Lowe
educa ion
0.08 7.08 10 70.04 0.313 0.08 6.13 10 7
Highe
educa ion
0.09 1.19 1080.08 0.450 0.09 1.20 10 8
s8023401
(15:48703823)
FBN1 G/A 0.87/0.95 JMA 1.66 10 90.180 0.572 0.979 2.85 10 90.495
Lowe
educa ion
0.15 4.40 10 80.06 0.304 0.13 8.17 10 8
Highe
educa ion
0.16 7.61 10 11 0.03 0.828 0.14 2.02 10 9
s16949788
(15:66590037)
DIS3L-
MAP2K1
T/C 0.91/0.94 JMA 1.34 1080.721 0.0042 0.219 2.19 10 80.245
Lowe
educa ion
0.15 1.35 1060.21 0.103 0.13 4.88 10 6
Highe
educa ion
0.17 1.89 10 90.59 0.014 0.16 3.90 10 9
s10880855
(12:46144855)
ARID2-SNAT1 T/C 0.51/0.43 JMA 7.83 1070.790 0.019 0.779 4.38 10 80.867
Lowe
educa ion
0.09 1.26 10 70.06 0.067 0.09 8.42 109
Highe
educa ion
0.07 1.60 10 50.16 0.033 0.07 3.55 10 6
s10853531
(18:42824449)
SLC14A2 G/A 0.80/0.83 JMA 7.82 10 60.052 0.0023 0.812 2.54 1080.111
Lowe
educa ion
0.11 1.27 10 60.15 9.01 10 40.11 3.38 10 9
Highe
educa ion
0.08 2.12 10 60.11 0.288 0.09 7.14 10 6
b,b-coe ficien co esponds o he e ec in sphe ical equi alen (diop es) o 1 addi ional copy o he isk allele in he highe o lowe educa ion g oup. FREQ, allele equency o he isk allele in
Eu opean/Asian coho s; JMA, join me a-analysis on SNP e ec and SNP educa ion in e ac ion e ec on sphe ical equi alen ; P
he
,P- alue o he es o he e ogenei y a each SNP; SNP,
single-nucleo ide polymo phism. Allele, isk allele/o he allele.
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Ma an’s synd ome, a diso de o connec i e issue a ec ing he
ocula , skele al and ca dio ascula sys ems45. As a candida e gene
o myopia, a emp s o s udy i s associa ion wi h myopia
p e iously p oduced inconclusi e esul s46,47, p obably owing,
in pa , o unde powe ed s udies wi h insu ficien sample sizes.
Using da a om a la ge mul i-e hnic popula ion, ou esul s
suppo he ole o FBN1 in myopia de elopmen .
The genome-wide significan SNPs om he JMA app oach did
no exhibi any in e ac ions wi h educa ion in Eu opeans, in
con as o he significan in e ac i e e ec among Asians. In
pa icula , he G E in e ac ions a AREG,GABRR1 and PDE10A
we e only e iden in Asian popula ions. The e a e a numbe o
possible easons o he obse ed di e ences. Fi s , he a ia ion
o LD pa e ns and join e ec s o gene ic a ian s migh a ec
he ans e abili y o G E signals ac oss popula ions. Simila LD
pa e ns we e seen a GABRR1 and PDE10A egions ac oss
popula ions whe eas a long s e ch o LD flanking AREG was
p esen only in Asian popula ions (Supplemen a y Fig. 5). As he
ue causal a ian s ans e able ac oss popula ions a e p obably
no implica ed in ou s udy, he iden ified no el myopia isk loci
p o ide a much-needed s a ing poin o ollow-up and
unc ional downs eam analyses. Second, we used educa ion le el
in adul s as a su oga e measu e o he unde lying isk ac o s o
influencing e ac i e de elopmen . Ideally, nea wo k in ensi y
would be measu ed p ospec i ely in child en be o e he onse o
myopia. S udies included in ou analyses do no ha e addi ional
da a on ele an childhood exposu es. Thus, he bes a ailable
su oga e measu e o cumula i e nea wo k exposu e in adul
coho s is educa ional le el. We ne e heless belie e ha
educa ion is a highly eliable p oxy o he ele an exposu es
unde lying e ac i e de elopmen and is uni e sally associa ed
wi h e ac i e e o in ou s udy. Thi d, he di e ences o G E
in e ac ions in Asian e sus Eu opeans may eflec quan i a i e
di e ences in nea wo k in ensi y du ing childhood. Fo example,
6- and 7- yea -old child en in England and Aus alia epo ed less
nea wo k ac i i y ou side o school (1.0–2.3 h pe day)48,49
compa ed wi h child en in Singapo e and China (2.7–3.5 h pe
day)50,51. A simila end was obse ed in olde child en48,52–55.
We hus specula e ha he o al exposu e o nea wo k ac i i y
may be g ea e in Eas Asians compa ed wi h Eu opean-de i ed
popula ions wi h he same le els o educa ion; hence, G E
in e ac ion es ima es would end o be infla ed in Asian
popula ions compa ed wi h Eu opean g oups. Fou h, o he
en i onmen al ac o s such as ou doo ac i i ies could also
in e ac wi h genes. Eas Asian child en end o ha e less exposu e
o ou doo ac i i ies compa ed wi h hei Eu opean pee s56.
Howe e , he majo i y o adul coho s did no epo ime
ou doo s and hus could no be accoun ed o in he cu en
s udy. Finally, he popula ion mean o e ac i e e o is less
myopic in Eu opeans (0.10 D) e sus Asians ( 0.60 D). O no e,
o he p e iously known myopia loci, he magni udes o
in e ac ion e ec s we e ou old la ge on a e age in Asians
han in Eu opeans (Supplemen a y Fig. 2). The impac o G E
in e ac ions may be seen a ce ain se e i y le els o myopia.
The isk alleles o s12511037 in AREG, s1321556 in GABRR1
and s12206610 in PDE10A had no o weak influence on myopic
shi in he lowe educa ion g oup compa ed wi h he highe
educa ion g oup. This sugges s ha he he edi a y p edisposi ion
o myopia could be la en o he isk allele ca ie s, i hey a e less
exposed o he myopiagenic en i onmen associa ed wi h high-
le el educa ion. A lack o s ong SNP nea wo k associa ions in
child en migh be due o he inadequa e s a is ical powe in
paedia ic coho s o ela i ely small sample sizes, o he
possibili y ha en i onmen al isk exposu es o he han nea
wo k migh unde lie he SNP educa ion in e ac ion seen in he
adul Asian samples.
In summa y, we iden ified nine no el loci associa ed wi h
e ac i e e o in a la ge mul i-e hnic coho s udy by GEWIS
app oach. Ou da a p o ide e idence ha specific gene ic a ian s
in e ac wi h educa ion, o influence e ac i e de elopmen , and
u he suppo a ole o GABA neu o ansmi e signalling in
myopia de elopmen . These findings p o ide p omising
Table 3 | Th ee gene ic loci associa ed wi h sphe ical equi alen wi h a significan SNP educa ion in e ac ion in Asians and
esul s in Eu opean popula ions.
SNP (Ch :BP) Gene Allele FREQ Subg oup Asians
(n¼10,315)
Eu opeans
(n¼40,036)
bP- alue P
he
bP- alue P
he
s12511037*
(4:75334864)
AREG C/T 0.91/0.95 Lowe educa ion 0.07 0.243 0.05 0.323
Highe
educa ion
0.70 1.97 10 10 0.03 0.579
SNP educa ion 0.89 6.87 10 11 0.704 0.02 0.176 0.284
JMA 5.55 1010 0.405 0.527 0.186
s13215566
(6:89918638)
GABRR1 C/G 0.94/0.84 Lowe educa ion 0.13 0.030 0.03 0.258
Highe
educa ion
0.68 1.46 10 80.01 0.817
SNP educa ion 0.56 8.48 1050.134 0.02 0.459 0.457
JMA 3.81 1080.122 0.502 0.630
s12206610
6:166016800
PDE10A C/T 0.90/0.87 Lowe educa ion 0.16 0.008 0.01 0.759
Highe
educa ion
0.59 8.16 1080.01 0.810
SNP educa ion 0.72 2.32 1080.920 0.002 0.421 0.111
JMA 9.21 1090.902 0.954 0.305
b(highe educa ion/lowe educa ion), b-coe ficien co esponds o he e ec in sphe ical equi alen (diop es) o 1 addi ional copy o he e ec allele in he highe /lowe educa ion g oup; b
(SNP educa ion), b-coe ficien co esponds o he di e ence in sphe ical equi alen (diop es) o 1 addi ional copy o he e ec allele in he highe e sus lowe educa ion g oup; FREQ, allele equency
o he e ec allele in Asian/Eu opean coho s; JMA, join me a-analysis on SNP e ec and SNP educa ion in e ac ion e ec on sphe ical equi alen ; LD, linkage disequilib ium; P
he
,P- alue o he es
o he e ogenei y; SNP, single-nucleo ide polymo phism.
band P- alues o SNP educa ion in e ac ion we e calcula ed by he me a-analysis o conduc ing a 1d Wald’s es o single in e ac ion pa ame e . Allele is lis ed as e ec allele/o he allele.
*SNP s12511037 was no p esen in Eu opean s udies a e quali y con ol. He e we p esen he esul s o a p oxy SNP s1246413 (T/G, equency o isk allele T¼0.95) in LD wi h s12511037 ( 2¼0.97).
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candida e genes o ollow-up wo k and may lead o new gene ic
a ge s o he apeu ic in e en ions on myopia.
Me hods
S udy pa icipan s.Thi y- ou s udies om membe s o CREAM, comp ising
40,036 indi iduals o Eu opean ances y om 25 s udies and 10,315 indi iduals o
Asian ances y om 9 s udies, we e made a ailable o his analysis (Table 1 and
Supplemen a y No e 1). Indi iduals aged o20 yea s we e excluded and so we e
hose who had unde gone ca a ac su ge y, lase o o he in a-ocula p ocedu es
ha could al e e ac ion. Many o hese s udies we e also included in he p e ious
CREAM GWAS on sphe ical equi alen 8. All s udies adhe ed o he ene s o he
Decla a ion o Helsinki and we e app o ed by hei local esea ch e hics
commi ees. The exac names o he Ins i u ional Resea ch Boa d commi ees can
be ound unde Supplemen a y No e 2. All pa icipan s p o ided a signed consen
o m be o e he s a o he s udy.
Pheno yping and educa ion le els.All pa icipan s unde wen oph halmological
examina ions (Supplemen a y Table 1). Non-cycloplegic e ac ion was measu ed
by au o e ac ion and/o subjec i e e ac ion. Sphe ical equi alen was calcula ed
as he sphe e powe plus hal o he cylinde powe o each eye. The mean
sphe ical equi alen o he igh and le eyes was used as a quan i a i e ou come.
When da a om only one eye was a ailable, he sphe ical equi alen o ha eye was
used. Fo each s udy, he pa icipan s epo ed he highes le el o educa ion
achie ed o he yea s o schooling h ough a sel - epo ed ques ionnai e, o in an
in e iew.
We dicho omized educa ion o all pa icipan s in each s udy. The highe
educa ion g oup consis ed o hose who had achie ed he highes educa ional le el
o A-le els, high school (highe seconda y educa ion), oca ional aining ( o
example, diploma), uni e si y deg ee o hose wi h Z12 yea s spen in o mal
educa ion (beginning om fi s g ade). Those who had achie ed he highes
educa ional le el o O-le el, middle school (lowe seconda y educa ion) o hose
wi h o12 yea s o o mal educa ion we e classified in o he lowe educa ion g oup.
I bo h numbe o o mal s udy yea s and educa ion le els we e a ailable in he
coho , we classified pa icipan s based on yea s o o mal educa ion. Fo he ou
coho s o ela i ely young Eu opean pa icipan s (BATS, DCCT, RAINE and
WESDR; o al n¼2,349), almos all o hem had comple ed 12 o mo e yea s o
schooling. We hus chose o ca ego ize indi iduals wi h e ia y o uni e si y
educa ion as he highe educa ion g oup in hese s udies. Sensi i i y analysis
excluding hese ou coho s did no app eciably change ou me a-analysis esul s.
Geno yping and impu a ion.De ailed in o ma ion on he geno yping pla o ms
and QC p ocedu es o each s udy is p o ided in Supplemen a y Table 2 and
Supplemen a y No e 1. Each s udy applied s ingen QC fil e s o GWAS. In
gene al, duplica e DNA samples, indi iduals wi h low call a e (o95%), gende
misma ch o e hnic ou lie s we e excluded. SNPs we e excluded i low geno yping
call a e (45% missingness), monomo phic SNPs, wi h mino allele equency
(MAF) o1% o in Ha dy–Weinbe g disequilib ium (Po106). A e QC fil e ing,
he a ay geno ypes o each s udy we e impu ed using he 1000 Genomes P ojec
da a as e e ence panels (build 37, phase 1 elease, Ma ch 2012) wi h he so wa e
Minimac57 o IMPUTE2 ( e . 58). App oxima ely six million SNPs ha passed
impu a ion quali y h esholds (MACH: 240.5 o IMPUTE in o sco e 40.5) and
wi h MAF Z5% we e eligible o he me a-analysis (Supplemen a y Table 2).
S a is ical models.Fo each s udy, a linea eg ession model o each geno yped
o impu ed SNP was cons uc ed wi h he mean sphe ical equi alen as he ou -
come. We assumed an addi i e gene ic model whe e he numbe o isk alleles is an
o dinal a iable (0, 1 and 2) o di ec ly geno yped SNPs o a con inuous a iable
o allele dosage p obabili y anging om 0 o 2 o impu ed SNPs. The p ima y
analy ic model included SNP, educa ion and SNP educa ion in e ac ion e m, as
well as age and sex as co a ia es. Addi ional adjus men s o he op p incipal
componen s o genomic ma ke a ia ions we e pe o med in indi idual s udies
when applicable ( ha is, when he e was e idence o popula ion s a ifica ion).
We used he ollowing addi i e gene ic model o es o a join e ec o SNP
(b
SNP
) and SNP educa ion in e ac ion (b
SNP educa ion
) on mean sphe ical
equi alen :
Y¼b0þbSNPSNP þbeduca ioneduca ion þbSNPeduca ionSNPeduca ion þbCco þe
ð1Þ
whe e Yis he mean sphe ical equi alen and educa ion is a dicho omous a iable
(0 ¼lowe educa ion g oup and 1 ¼highe educa ion g oup); co is a se o
co a ia es such as age, sex and fi s op fi e p incipal componen s when applicable.
Fo amily-based s udies, he kinship ma ix was es ima ed empi ically om he
SNP da a and included as a andom e ec in he gene alized mixed model59.To
es an e ec o SNP educa ion in e ac ion, we assessed b
SNP educa ion
om
equa ion (1).
The linea eg ession analyses in each s udy we e conduc ed wi h Quickes o
P obABEL o he un ela ed samples and MixABEL o amily-based da a. The
command ‘ obus ’ was used in he abo e so wa e o calcula e he obus
(‘sandwich’, Hube -Whi e) s.e. o b
SNP
and b
SNP educa ion
, and e o co a iance
o b, o co ec he po en ial infla ion o alse posi i e a e o he in e ac ion
P- alue60.
In addi ion, each s udy also es ed he main e ec o educa ion on sphe ical
equi alen by adjus ing o age and gende using he linea eg ession model:
Y¼b0þbeduca ioneduca ion þbCco þeð2Þ
whe e he defini ion o each a iable is he same as in equa ion (1). We pe o med
me a-analysis o he educa ion e ec s on mean sphe ical equi alen in Eu opeans,
Asians (Singapo e Chinese e sus o he s) and combined da a using a fixed-e ec
model wi h in e se- a iance weigh ing (R package ‘me a’).
GEWIS join me a-analyses.We adop ed he JMA app oach17,61, o
simul aneously es bo h SNP main e ec s and SNP educa ion in e ac ions o
sphe ical equi alen wi h a fixed-e ec model, using SNP and SNP educa ion
eg ession coe ficien s (b
SNP
and b
SNP educa ion
, espec i ely) and a b’s co a iance
ma ix om each s udy. A Wald’s s a is ic, ollowing a w2-dis ibu ion wi h wo
deg ees o eedom, was used o es he join significance o he b
SNP
and
b
SNP educa ion
. The JMA was pe o med wi h METAL62, as p e iously desc ibed by
Manning e al.61. A Coch an’s Q- es was used o assess he e ogenei y o he
b-coe ficien s ac oss s udies o he SNP and in e ac ion e ec s. To es o
in e ac ion be ween he SNP and educa ion, we conduc ed a seconda y me a-
analysis o he SNP educa ion in e ac ion e ec s o sphe ical equi alen
(b
SNP educa ion
, one deg ee o eedom), wi h a fixed-e ec s model using in e se-
a iance weigh ing in METAL; his is a adi ional me a-analysis o in es iga e
SNP educa ion in e ac ions pe se. E ec s and s.e. o he SNP e ec on sphe ical
equi alen in he lowe educa ion g oup (b
SNP
) and highe educa ion g oup
(b
SNP
þb
SNP educa ion
) we e de i ed om he JMA ou pu 61. We used he P- alue
o 5 10 8as a significan h eshold o JMA es . Fo he SNP and
SNP educa ion e ec s o he iden ified op loci, he P- alue h eshold o
significance was se a 0.0055 ¼0.05/9 (9 index SNPs unde lying analyses).
We pe o med a me a- eg ession o explo e sou ces o he e ogenei y in ou
me a-analysis o h ee loci showing G E in e ac ions (R package ‘me a o ’).
Me a- eg ession included he ollowing s udy-specific a iables as co a ia es: s udy
sample size, p opo ion o indi iduals in he highe educa ion g oup, a e age
sphe ical equi alen , educa ion main e ec s on sphe ical equi alen (highe
educa ion le el e sus lowe ), e hnici y (Asian e sus Eu opean), s udy design
(independen samples e sus amily-based s udies), s udy yea and a e age age.
Me a- eg ession was also conduc ed o es he old changes o he in e ac ion
b-coe ficien s in Asians e sus Eu opeans o he 39 known myopia loci.
The s udy-specific genomic con ol infla ion ac o s l
gc
o he join es o SNP
and in e ac ion e ms anged om 1.009 o 1.125 wi h an a e age o 1.019
(Supplemen a y Table 2), calcula ed by he a io o he obse ed median w2di ided
by he expec ed median o he 2d w2-dis ibu ion (1.382). Genomic con ol
co ec ion was applied o each indi idual s udy63. Fo s udies o small sample sizes
(no500) wi h l
gc
41.05, we u he , be o e s a ing he me a-analysis, excluded
SNPs showing significan join P- alue o1105bu nei he he SNP no
SNP educa ion e ec s suppo ed such an associa ion. Quan ile–quan ile plo s
showed only modes infla ion o he es s a is ics in he JMA es (Eu opeans:
l
gc
¼1.081; Asians: l
gc
¼1.053; Combined: l
gc
¼1.092; Supplemen a y Fig. 1),
simila o p e ious GEWIS s udies wi h compa able sample sizes18,19.Weexcludeda
small numbe o ma ke s in he me a-analysis wi h P
he
o0.0001. The l
gc
o he
SNP educa ion in e ac ion e m in he indi idual s udies anged om 1.01 o 1.08,
indica ing li le e idence o es s a is ic infla ion on SNPeduca ion e ec o each
s udy.
Anno a ion o gene ic a ian s and gene exp ession in humans.The
coo dina es and a ian iden ifie s a e epo ed on he NCBI B37 (hg19) genome
build and anno a ed using UCSC Genome B owse 64. We iden ified a ian s wi hin
each o he LD blocks ( 2Z0.8) in Eu opean and Asian popula ions o he 1000
Genomes P ojec (100 kb flanking he op SNP a each locus), o apply unc ional
anno a ions o ansc ip ion egula ion using HaploReg65 and Encyclopedia o
DNA Elemen s66 da a. We also gene a ed unca ional associa ion and co-
exp ession ne wo k using GeneMANIA67, o de e mine whe he he disease- ela ed
genes iden ified in his s udy and p e ious GWAS7,8 a e unc ionally connec ed.
To assess gene exp ession in human issues, we examined he Ocula Tissue
Da abase and he EyeSAGE da abase31,68. The es ima ed gene and exome-le el
abundances a e a ailable online. No maliza ion o gene exp ession used he P obe
Loga i hmic In ensi y E o me hod wi h genomic con ol-backg ound
co ec ion31. Rela ionships be ween geno ype and cis egula ion o gene exp ession
le els (Supplemen a y Table 9) we e assessed using exp ession quan i a i e ai
locus associa ions in mul iple human issues om UK samples34, as well as gene
exp ession p ofiles ob ained om GTExPo al da abase69.
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