Tobacco
E idence o la ge-scale gene-by-smoking
in e ac ion e ec s on pulmona y unc ion
Hugues Ascha d,
1,2*
Ma in D Tobin,
3,4
Dana B Hancock,
5
Da id Sku nik,
6
Akshay Sood,
7
Alan James,
8,9
Albe Ve non Smi h,
10,11
Ani W Manichaikul,
12,13
A chie Campbell,
14,15
B am P P ins,
16
Ca oline Haywa d,
17
Daan W Lo h,
18
Da id J Po eous,
14,15
Da id P S achan,
19
Ele he ia Zeggini,
16
Geo ge T O’Conno ,
20,21
Guy G B usselle,
18,22,23
H Ma ike Boezen,
24,25
Holge Schulz,
26,27
Ian J Dea y,
28,29
Ian P Hall,
30
Igo Rudan
31
Jaakko Kap io,
32,33,34
James F Wilson,
31,17
Jemma B Wilk,
20
Jenni e E Hu man,
17
Jing Hua Zhao,
35,36
Kim de Jong,
24,25
Leo-Pekka Lyy ik€
ainen,
37,38
Louise V Wain,
3,4
Ma jo-Rii a Ja elin
39,40,41,42
Mika K€
aho¨ nen,
43
My iam Fo nage,
44
Oz en Polasek
31,45
Pa icia A Cassano,
46,47
R G aham Ba ,
48
Rajesh Rawal
49,50,51
Sa ah E Ha is,
14,28
Sina A Gha ib,
52
S e an En o h,
53
Susan R Heckbe ,
55
Te ho Leh im€
aki,
37,38
Ul Gyllens en,
53
Unde s anding Socie y Scien i ic G oup, Vic o ia E Jackson,
3
Vilmundu Gudnason,
10,11
Wenbo Tang,
46,55
Jose´e Dupuis,
20,56
Ma 
ıa
Sole A igas,
3
Ami D Joshi,
1,2,57
S ephanie J London
58†
and
Pe e K a
1,2†
1
Depa men o Epidemiology, Ha a d TH Chan School o Public Heal h, Bos on, MA, USA,
2
P og am in
Gene ic Epidemiology and S a is ical Gene ics, Ha a d TH Chan School o Public Heal h, Bos on, MA,
USA,
3
Gene ic Epidemiology G oup, Depa men o Heal h Sciences, Uni e si y o Leices e , Leices e ,
UK,
4
Na ional Ins i u e o Heal h Resea ch, Leices e Respi a o y Biomedical Resea ch Uni , Glen ield
Hospi al, Leices e , UK,
5
Beha io al and U ban Heal h P og am, Beha io al Heal h and C iminal Jus ice
Resea ch Di ision, Resea ch T iangle Ins i u e (RTI) In e na ional, Resea ch T iangle Pa k, NC, USA,
6
Di ision o In ec ious Diseases, B igham and Women Hospi al, Ha a d Medical School, Bos on, MA,
USA,
7
Di ision o Pulmona y, C i ical Ca e and Sleep Medicine, Depa men o In e nal Medicine,
Uni e si y o New Mexico School o Medicine, Albuque que, NM, USA,
8
Depa men o Pulmona y
Physiology and Sleep Medicine, Si Cha les Gai dne Hospi al, Nedlands, Aus alia,
9
School o Medicine
and Pha macology, Uni e si y o Wes e n Aus alia, C awley, Aus alia,
10
Icelandic Hea Associa ion,
Kopa ogu , Iceland,
11
Facul y o Medicine, Uni e si y o Iceland, Reykja ik, Iceland,
12
Cen e o Public
Heal h Genomics, Uni e si y o Vi ginia, Cha lo es ille, VA, USA,
13
Depa men o Public Heal h
Sciences, Di ision o Bios a is ics and Epidemiology, Uni e si y o Vi ginia, Cha lo es ille, VA, USA,
14
Cen e o Genomic & Expe imen al Medicine, Ins i u e o Gene ics & Molecula Medicine, Uni e si y
o Edinbu gh, Edinbu gh, UK,
15
Gene a ion Sco land, Cen e o Genomic and Expe imen al Medicine,
Uni e si y o Edinbu gh, Edinbu gh, UK,
16
Depa men o Human Gene ics, Wellcome T us Sange
V
CThe Au ho 2017. Published by Ox o d Uni e si y P ess on behal o he In e na ional Epidemiological Associa ion 894
This is an Open Access a icle dis ibu ed unde he e ms o he C ea i e Commons A ibu ion License (h p://c ea i ecommons.o g/licenses/by/4.0/), which pe mi s
un es ic ed euse, dis ibu ion, and ep oduc ion in any medium, p o ided he o iginal wo k is p ope ly ci ed.
In e na ional Jou nal o Epidemiology, 2017, 894–904
doi: 10.1093/ije/dyw318
Ad ance Access Publica ion Da e: 12 Janua y 2017
O iginal a icle
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by Tampe e Uni e si y Lib a y use
on 09 Oc obe 2017
Ins i u e, Hinx on, UK,
17
MRC Human Gene ics Uni , Ins i u e o Gene ics and Molecula Medicine,
Uni e si y o Edinbu gh, Edinbu gh, UK,
18
Depa men o Epidemiology, E asmus Medical Cen e ,
Ro e dam, The Ne he lands,
19
Popula ion Heal h Resea ch Ins i u e, S Geo ge’s Uni e si y o London,
London, UK,
20
The Na ional Hea , Lung, and Blood Ins i u e’s F amingham Hea S udy, F amingham, MA,
USA,
21
The Pulmona y Cen e , Depa men o Medicine, Bos on Uni e si y School o Medicine, Bos on,
MA, USA,
22
Depa men o Respi a o y Medicine, Ghen Uni e si y Hospi al, Ghen , Belgium,
23
Depa men o Respi a o y Medicine, E asmus Medical Cen e , Ro e dam, The Ne he lands,
24
Uni e si y o G oningen, Uni e si y Medical Cen e G oningen, Depa men o Epidemiology, G oningen,
The Ne he lands,
25
Uni e si y o G oningen, Uni e si y Medical Cen e G oningen, G oningen Resea ch
Ins i u e o As hma and COPD, G oningen, The Ne he lands,
26
Ins i u e o Epidemiology I, Helmhol z
Zen um Mu¨nchen, Ge man Resea ch Cen e o En i onmen al Heal h, Neuhe be g, Ge many,
27
Comp ehensi e Pneumology Cen e Munich (CPC-M), Membe o he Ge man Cen e o Lung
Resea ch, Munich, Ge many,
28
Cen e o Cogni i e Ageing and Cogni i e Epidemiology, Uni e si y o
Edinbu gh, Edinbu gh, UK,
29
Depa men o Psychology, Uni e si y o Edinbu gh, Edinbu gh, UK,
30
Di ision
o Respi a o y Medicine, Uni e si y o No ingham, Queen’s Medical Cen e, No ingham, UK,
31
Cen e o
Global Heal h Resea ch, Ushe Ins i u e o Popula ion Heal h Sciences and In o ma ics, Uni e si y o
Edinbu gh, Edinbu gh, UK,
32
Depa men o Public Heal h, Uni e si y o Helsinki, Helsinki, Finland,
33
Ins i u e o Molecula Medicine, Uni e si y o Helsinki, Helsinki, Finland,
34
Na ional Ins i u e o Heal h
and Wel a e, Depa men o Heal h, Helsinki, Finland,
35
MRC Epidemiology Uni , Uni e si y o Camb idge
School o Clinical Medicine, Camb idge, UK,
36
Ins i u e o Me abolic Science, Biomedical Campus,
Camb idge, UK,
37
Depa men o Clinical Chemis y, Fimlab Labo a o ies, Tampe e, Finland,
38
Depa men
o Clinical Chemis y, Uni e si y o Tampe e School o Medicine, Tampe e, Finland,
39
Depa men o
Epidemiology and Bios a is ics, MRC–PHE Cen e o En i onmen & Heal h, School o Public Heal h,
Impe ial College London, UK,
40
Cen e o Li e Cou se Epidemiology, Facul y o Medicine, Uni e si y o
Oulu, Oulu, Finland,
41
Biocen e Oulu, Uni e si y o Oulu, Oulu, Finland,
42
Uni o P ima y Ca e, Oulu
Uni e si y Hospi al, Oulu, Finland,
43
Depa men o Clinical Physiology, Uni e si y o Tampe e and
Tampe e Uni e si y Hospi al, Tampe e, Finland,
44
B own Founda ion Ins i u e o Molecula Medicine,
Uni e si y o Texas Heal h Science Cen e a Hous on, Hous on, TX, USA,
45
Facul y o Medicine,
Uni e si y o Spli , Spli , C oa ia,
46
Di ision o Nu i ional Sciences, Co nell Uni e si y, I haca, NY, USA,
47
Depa men o Heal hca e Policy and Resea ch, Weill Co nell Medical College, NY, NY, USA,
48
Depa men s o Medicine and Epidemiology, Columbia Uni e si y Medical Cen e ,
49
Ins i u e o Gene ic
Epidemiology, Helmhol z Zen um Mu¨nchen, Ge man Resea ch Cen e o En i onmen al Heal h,
Neuhe be g, Ge many,
50
Resea ch Uni o Molecula Epidemiology, Helmhol z Zen um Mu¨nchen,
Ge man Resea ch Cen e o En i onmen al Heal h, Neuhe be g, Ge many,
51
Ins i u e o Epidemiology II,
Helmhol z Zen um Mu¨nchen, Ge man Resea ch Cen e o En i onmen al Heal h, Neuhe be g, Ge many,
52
Compu a ional Medicine Co e a Cen e o Lung Biology, Di ision o Pulmona y & C i ical Ca e
Medicine, Uni e si y o Washing on, Sea le, WA,
53
Depa men o Immunology, Gene ics and Pa hology,
Uppsala Uni e si e , Science o Li e Labo a o y, Uppsala, Sweden,
54
Ca dio ascula Heal h Resea ch
Uni and Depa men o Epidemiology, Uni e si y o Washing on, Sea le, WA, USA,
55
Boeh inge
Ingelheim Pha maceu icals, Inc., Ridge ield, CT, USA,
56
Depa men o Bios a is ics, Bos on Uni e si y
School o Public Heal h, Bos on, MA, USA,
57
Di ision o Gas oen e ology, Massachuse s Gene al
Hospi al, Bos on, MA, USA. Human Se ices, Resea ch T iangle Pa k, NC, USA and
58
Epidemiology
B anch, Na ional Ins i u e o En i onmen al Heal h Sciences, Na ional Ins i u es o Heal h, US
Depa men o Heal h and Human Se ices, Resea ch T iangle Pa k, NC, USA
*Co esponding au ho . Depa men o Epidemiology, Ha a d School o Public Heal h, Building 2, Room 205, 665
Hun ing on A enue, Bos on, MA 02115, USA. E-mail: [email p o ec ed]
†
These au ho s con ibu ed equally o his wo k.
Accep ed 10 Oc obe 2016
In e na ional Jou nal o Epidemiology, 2017, Vol. 46, No. 3 895
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by Tampe e Uni e si y Lib a y use
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Abs ac
Backg ound: Smoking is he s onges en i onmen al isk ac o o educed pulmona y
unc ion. The gene ic componen o a ious pulmona y ai s has also been demon-
s a ed, and a leas 26 loci ha e been ep oducibly associa ed wi h ei he FEV
1
( o ced
expi a o y olume in 1 second) o FEV
1
/FVC (FEV
1
/ o ced i al capaci y). Al hough he
main e ec s o smoking and gene ic loci a e well es ablished, he ques ion o po en ial
gene-by-smoking in e ac ion e ec emains unanswe ed. The aim o he p esen s udy
was o assess, using a gene ic isk sco e app oach, whe he he e ec o hese 26 loci on
pulmona y unc ion is in luenced by smoking.
Me hods: We e alua ed he in e ac ion be ween smoking exposu e, conside ed as ei he
e e s ne e o pack-yea s, and a 26-single nucleo ide polymo phisms (SNPs) gene ic
isk sco e in ela ion o FEV
1
o FEV
1
/FVC in 50 047 pa icipan s o Eu opean ances y
om he Coho s o Hea and Aging Resea ch in Genomic Epidemiology (CHARGE) and
Spi oMe a conso ia.
Resul s: We iden i ied an in e ac ion (b
in
¼–0.036, 95% con idence in e al, –0.040 o
–0.032, P¼0.00057) be ween an unweigh ed 26 SNP gene ic isk sco e and smoking s a-
us (e e /ne e ) on he FEV
1
/FVC a io. In in e p e ing his in e ac ion, we showed ha
he gene ic isk o alling below he FEV
1
/FVC h eshold used o diagnose ch onic ob-
s uc i e pulmona y disease is highe among e e smoke s han among ne e smoke s.
A eplica ion analysis in wo independen da ase s, al hough no s a is ically signi ican ,
showed a simila end in he in e ac ion e ec .
Conclusions: This s udy highligh s he bene i o using gene ic isk sco es o iden i ying
in e ac ions missed when s udying indi idual SNPs and shows, o he i s ime, ha
pe sons wi h he highes gene ic isk o low FEV
1
/FVC may be mo e suscep ible o he
dele e ious e ec s o smoking.
Key wo ds: FEV
1
/FVC, smoking, gene–en i onmen in e ac ion, gene ic isk sco e
In oduc ion
Spi ome ic measu es o pulmona y unc ion, such as he
o ced expi a o y olume in 1 second (FEV
1
) o i s a io
wi h he o ced i al capaci y (FEV
1
/FVC), o m he basis o
he diagnosis o ch onic obs uc i e pulmona y disease
(COPD).
1–3
Pulmona y unc ion measu es a e also used clin-
ically o moni o se e i y and con ol o as hma and o he e-
spi a o y diseases and a e independen isk ac o s o
mo ali y.
1–3
Pulmona y unc ion is s ongly in luenced by
ciga e e smoking and by mul iple low-pene ance gene ic
a ian s. Indeed, genome-wide associa ion s udies (GWAS)
o ma ginal gene ic e ec s (i.e. no including in e ac ion e -
ec s be ween gene ic a ian s and smoking) ha e iden i ied
a leas 26 loci associa ed wi h FEV
1
o FEV
1
/FVC in he
gene al popula ion.
4
Howe e , he in e play be ween gene ic
ac o s and en i onmen al exposu es has no been well
Key Messages
•Spi ome ic measu es o pulmona y unc ion a e in luenced by bo h smoking and gene ics. This pape epo s a gen-
e ic isk sco e-by-e e smoking in e ac ion on FEV
1
/FVC ( o ced expi a o y olume in 1 second/ o ced i al capaci y).
•In indi iduals o Eu opean ances y, he educ ion in FEV
1
/FVC as a esul o smoking was g ea e among indi iduals
who a e gene ically p edisposed o lowe FEV
1
/FVC a io.
•Gene ic isk sco e-by-e e smoking in e ac ion can allow he iden i ica ion o subg oups in he popula ion whose gen-
e ic backg ound makes hem mo e suscep ible o he dele e ious e ec s o smoking.
896 In e na ional Jou nal o Epidemiology, 2017, Vol. 46, No. 3
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es ablished o pulmona y unc ion o i s associa ed ai s.
Mo e b oadly, al hough conside able e o s ha e been made
o iden i y in e ac ion e ec s be ween gene ic a ian s and
en i onmen al exposu es ac oss he wide ange o human
ai s and diseases,
5,6
such in es iga ions ha e been mos ly
unsuccess ul in de ec ing obus gene–en i onmen in e -
ac ions.
5,7
The well-es ablished e ec o ciga e e smoking
on nume ous human heal h ou comes
8
makes i a se ious
candida e o iden i ica ion o no el gene–en i onmen in e -
ac ions, especially o pulmona y ai s.
Hypo hesizing he p esence o single nucleo ide polymo ph-
ism (SNP)-by-smoking in e ac ion, Hancock e al.
9
pe o med
a genome-wide in e ac ion s udy o pulmona y unc ion, mod-
elling single SNP main e ec s and hei in e ac ions wi h
smoking in 50 047 pa icipan s o Eu opean ances y ac oss
19 s udies wi hin he Coho s o Hea and Aging Resea ch
in Genomic Epidemiology (CHARGE)
10
and Spi oMe a con-
so ia
11
— he la ges genome-wide in e ac ion s udy o pul-
mona y unc ion as modi ied by smoking o da e. Howe e ,
a he han ocusing on he in e ac ion e ec s pe se, hey pe -
o med a me a-analysis o he join es o SNP main e ec s
and SNP-by-smoking in e ac ion e ec s o imp o e powe o
iden i ying gene ic a ian s associa ed wi h pulmona y unc-
ion.
12,13
Al hough hey epo ed new candida e a ian s based
on his join es , he s udy did no iden i y any SNPs wi h
genome-wide signi ican in e ac ion wi h smoking.
He e, we explo ed gene-by-smoking in e ac ion e ec s
limi ed o gene ic a ian s p e iously ound o be associ-
a ed wi h pulmona y unc ion in s anda d ma ginal e ec s
GWAS,
4
he e o e no including he new a ian s epo ed
by Hancock e al.
9
based on he join es o main e ec s
plus in e ac ion. Speci ically, we aimed o de e mine
whe he smoking modi ies he e ec o es ablished gene ic
a ian s when conside ed singly o in combina ion using a
gene ic isk sco e summa izing he gene ic p edisposi ion
o abno mal pulmona y unc ion. The p ima y mo i a ion
o using gene ic isk sco e is s a is ical powe .
14,15
Indeed,
se e al gene ic isk sco e-by-exposu e in e ac ions ha e al-
eady been iden i ied in cases whe e single SNPs did no
show e idence o s a is ically signi ican in e ac ions.
16–21
Gene ic isk sco e-by-exposu e in e ac ion es ing expands
on he p inciple o omnibus es while le e aging he as-
sump ion ha , o a gi en choice o coded alleles, mos
in e ac ion e ec s will ha e he same di ec ion. This is
simila o bu den es s ha ha e been widely used o a e
a ian analysis
22
whe e a single pa ame e can accumula e
e idence o associa ion wi hou inc easing he numbe o
deg ees o eedom. When in e ac ion e ec s a e null on
a e age (i.e. i in e ac ion e ec s a e bo h nega i e and
posi i e so ha he sum o in e ac ion coe icien s end o
ze o), he single SNP app oach will gene ally ou pe o m
he isk sco e-based app oach. Con e sely, i in e ac ion
e ec s end o be in he same di ec ion, he isk sco e-
based app oach can ha e d ama ically highe powe .
14
Me hods
S udy sample
The p esen analysis elies on he Hancock e al.
9
genome-
wide me a-analysis o main gene ic e ec s plus in e ac ion
e ec s wi h smoking in ela ion o pulmona y unc ion
among 50 047 pa icipan s (56% women) o Eu opean an-
ces y om 19 s udies. The mean age was 53 yea s a he
ime o pulmona y unc ion es ing. App oxima ely 15%
we e cu en smoke s and 56% we e e e smoke s. Among
e e smoke s, he a e age pack-yea s o smoking was 21.
Supplemen a y Table 3 (a ailable as Supplemen a y da a
a IJE online) p o ides he main cha ac e is ics o he s ud-
ies included; comple e de ails o s udy-speci ic pulmona y
unc ion es ing p o ocols ha e been published.
4
Fo s ud-
ies wi h spi ome y a a single isi , we analysed FEV
1
/
FVC and FEV
1
measu ed a ha isi . Fo s udies wi h
spi ome y a mo e han one isi , measu emen s om he
baseline isi o he mos ecen examina ion wi h spi om-
e y da a was used. Smoking his o y (cu en , o me and
ne e smoking) was asce ained by ques ionnai e a he
ime o pulmona y unc ion es ing. Pack-yea s o smoking
we e calcula ed o cu en and pas smoke s by mul iply-
ing smoking amoun (packs pe day) and du a ion (yea s
smoked). App oxima ely 2.5 million au osomal SNPs we e
es ed o in e ac ion wi h smoking s a us (e e smoking s
ne e smoking) and pack-yea s, o wo ou comes: FEV
1
and FEV
1
/FVC (see nex sec ion). We also used wo inde-
penden da ase s o indi iduals o Eu opean ances y o
es o eplica ion. The i s eplica ion da ase included
8859 un ela ed indi iduals, and he second da ase
included 9457 amily-based indi iduals. The look-up was
done in he GWAS o ma ginal gene ic e ec s done sepa -
a ely in e e and ne e smoke as pa o a ecen me a-
analysis o FEV
1
and FEV
1
/FVC.
23
Single SNP-by-smoking in e ac ion
The analysis pe o med in his s udy used summa y s a is ics
da a om he a o emen ioned me a-analysis o 19 s udies
pe o med by Hancock e al.
9
In b ie , each o he 19 s udies
de i ed he esiduals o FEV
1
and FEV
1
/FVC a e eg essing
ou age, age
2
, sex, s anding heigh , p incipal componen
eigen ec o s o geno ypes and ec ui men si e i applicable.
The esiduals we e no malized using a ank-based in e se
no mal ans o ma ion. Single SNP in e ac ion e ec s we e
assessed using he ollowing model (see Supplemen a y No e,
a ailable as Supplemen a y da a a IJE online):
In e na ional Jou nal o Epidemiology, 2017, Vol. 46, No. 3 897
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Yb0þbGGþbGEkGEkþXl¼1...3bElEl;(1)
whe e b
G
and bEla e he main e ec o he SNP Gand ex-
posu e E
l
,bGEkis he in e ac ion e ec be ween Gand ex-
posu e E
k
, and b
0
he in e cep .
De ailed desc ip ion o s udies used in he eplica ion
analysis can be ound in Sole A igas e al.
23
In b ie , lin-
ea eg ession o age, age
2
, sex, heigh and p incipal com-
ponen s o popula ion s uc u e was unde aken on FEV
1
and FEV
1
/FVC sepa a ely o e e smoke s and ne e
smoke s. The esiduals we e no malized using a ank-
based in e se no mal ans o ma ion, again sepa a ely in
e e smoke s and ne e smoke s. These ans o med e-
siduals we e hen used as he pheno ype o associa ion
es ing unde an addi i e gene ic model in each exposu e
s a a. In e ence o he in e ac ion e ec s om he
exposu e-s a i ied analyses a e desc ibed in he
Supplemen a y No e (a ailable as Supplemen a y da a a
IJE online).
Mul i a ia e in e ac ion analysis o e iew
Fi s , we conside ed an unweigh ed gene ic isk sco e-by-
smoking in e ac ion whe e he isk sco e simply sums he
numbe o isk alleles (i.e. alleles associa ed wi h a lowe
pulmona y unc ion). This unweigh ed gene ic isk sco e is
mos powe ul when he in e ac ion e ec s ha e he same
di ec ion as ma ginal SNP e ec s (i.e. he ha m ul e ec s
o smoking a e magni ied in indi iduals wi h a gene ic p e-
disposi ion o educed pulmona y unc ion). Second, we
used a weigh ed gene ic isk sco e whe e SNPs we e
weigh ed by he absolu e alue o hei ma ginal e ec es i-
ma es ob ained om s age 1 sc eening o FEV
1
and FEV
1
/
FVC om Sole A igas e al.
4
(Supplemen a y Table 1,
a ailable as Supplemen a y da a a IJE online). This
weigh ing scheme is mos powe ul when he magni ude o
in e ac ion e ec s is p opo ional o he SNP ma ginal e -
ec s. Finally, o ou hi d mul i a ia e analysis, we
de i ed a s anda d omnibus es o all in e ac ion e ec s.
This es will e ain powe in he p esence o e ec s in bo h
di ec ions o o di e en magni udes. Al hough he e is
s ong co ela ion among he 12 es s pe o med ( hese
h ee models, conside ing in e ac ion wi h wo smoking
me ics, e e /ne e smoking o pack-yea s, o he wo pul-
mona y unc ion me ics FEV1 and FEV1/FVC), we used a
s ingen Bon e oni P- alue co ec ion h eshold o
410
–3
o accoun o mul iple es ing.
When aw da a a e a ailable, he weigh ed gene ic isk
sco e (GRS) is usually exp essed as GRS ¼R
m
[w
i
G
i
],
whe e mis he numbe o SNPs included in he gene ic isk
sco e and w¼(w
1
,..w
m
) a e he weigh s a ibu ed o each
single SNP. Following p e ious no a ion, he es o in e -
ac ion be ween he GRS and he exposu e E
k
can be
applied using he ollowing model:
Yc0þcGRS GRS þcINT GRS EkþXl¼1...3cEl
El;
(2)
whe e c
0
,c
GRS
,cEland c
INT
a e he in e cep , he main e -
ec o he GRS, he main e ec o he exposu e E
l
and he
in e ac ion e ec be ween E
k
and he GRS, espec i ely.
Howe e , because indi idual-le el da a we e no di ec ly
a ailable, we pe o med he es o c
INT
om summa y
s a is ics o in e ac ion e ec s using an in e se- a iance
weigh ed sum as p oposed by Ascha d.
14
The chi-squa e
o he in e ac ion e m c
INT
was de i ed as ollows:
2
in ¼Xi¼1...m
wi^
bGiEk
^
2
bGiEk
!
2
Xi¼1...m
w2
i
^ 2
bGiEk
;(3)
whe e ^
bGiEkand ^
2
bGiEk
a e he es ima ed e ec s and a i-
ance o he in e ac ion be ween he exposu e E
k
and he
SNP G
i
ob ained om Equa ion (1) and w
i
is he weigh
applied o SNP G
i
.Unde he null hypo hesis o no in e -
ac ion e ec , 2
in ollows a chi-squa ed dis ibu ion wi h
one deg ee o eedom.
The s anda d omnibus es o all in e ac ion e ec s con-
sis ed o e alua ing join ly aGEk¼ðaG1Ek;...;aGmEkÞ
om he model:
Ya0þXi¼1...m½aGiGi
þXi¼1...m½aGiEkGiEkþXl¼1...3aElEl;
(4)
whe e a0,aGi,aEland aGiEka e he in e cep , he main e -
ec s o SNP G
i
and he exposu e E
l
, and he in e ac ion e -
ec be ween G
i
and E
k
.Le e aging he independence
be ween he SNPs conside ed (a single SNP was selec ed
o each independen locus), we also de i ed he omnibus
es using summa y s a is ics. Unde his independence as-
sump ion, he G
i
E
k
in e ac ion e ms would also be in-
dependen s,
14
so ha i can be pe o med by summing he
chi-squa e om each uni a ia e in e ac ion es o o m a
chi-squa e wi h mdeg ees o eedom as ollows:
2
omnibus ¼Xi¼1...m
^
b2
GiEk
^
2
bGiEk
;(5)
whe e ^
bGiEkand ^
2
bGiEk
a e he es ima ed e ec s and
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a iance o he in e ac ion be ween he exposu e E
k
and
he SNP G
i
ob ained om Equa ion (1).
Rela i e isk in e e smoke s s ne e smoke s
GRS in e ac ion e ec s can u he be ansla ed in e ms o
isk p edic ion. Fo pulmona y unc ion, low FEV
1
o FEV
1
/
FVC inc eases he isk o dea h
24
and oge he hey o m he
basis o he diagnosis o COPD.
1–3
COPD s age 2 o highe
a e de ined by he Global Ini ia i e o Ch onic Obs uc i e
Lung Disease (GOLD) as FEV
1
/FVC <0.70 and
FEV
1
<80% o he p edic ed alue. Acco ding o ecen s ud-
ies,
2,25
be ween 5% and 20% o Eu opean ances y adul s
a eexpec ed oha eFEV
1
/FVC <0.70, depending on smok-
ing cha ac e is ics and age dis ibu ion. Se e al s udies a gue
o a mo e s ingen h eshold o de ine COPD
25,26
based on
lowe limi o no mal p edic ed alue, a he han a ixed ab-
solu e alue, o p e en disease misclassi ica ion.
To explo e he impac o in e ac ion e ec on he isk
o disease, we de i ed he ela i e isk (RR) o ha ing
FEV
1
/FVC below a gi en h eshold (1%, 5% and 20%) in
e e smoke s s ne e smoke s condi ional on he un-
weigh ed GRS. This quan i y is de ined as he join p ob-
abili y o ha ing bo h FEV
1
/FVC in he in e al [–1,
FEV
1
/FVC
up
] and he GRS in he in e al [GRS
low
,GRS
up
].
This can be exp essed as he ollowing in eg al:
ð
FEV1=FVCup
1 ð
GRSup
GRSlow
1ðyjg;eÞ 2ðgjeÞdy dg;(6)
whe e y,eand ga e FEV
1
/FVC, smoking s a us and he
GRS, espec i ely, and
1
and
2
a e he p obabili y densi y
unc ion o y and g. The de ailed de i a ion o he abo e
in eg al is a ailable as Supplemen a y da a a IJE online.
Resul s
We selec ed 26 loci p e iously ound o be associa ed wi h
FEV
1
o FEV
1
/FVC a genome-wide signi icance
(P<510
–8
) in ma ginal associa ion es s
4,11,27
(i.e. no
including in e ac ion e ec s wi h smoking exposu es) and
eplica ed in he GWAS by Sole A igas e al.,
4
he la ges
me a-analysis o ma ginal gene ic e ec conduc ed o
hese wo ai s in he gene al popula ion. Addi ional loci
o hese wo pheno ypes ha e been iden i ied in wo ecen
s udies.
28,29
Howe e , hese new loci we e no included in
ou analysis because bo h hese s udies used a la ge coho
asce ained h ough smoking s a us. Fo each o he 26 se-
lec ed loci, we choose he SNP wi h he s onges e idence
o associa ion (i.e. smalles P- alue) wi h each o hese
pheno ypes. The inal lis included 26 SNPs pe pheno ype,
wi h only wo SNPs being di e en be ween FEV
1
and
FEV
1
/FVC as p e iously epo ed
4
(Supplemen a y Table
1, a ailable as Supplemen a y da a a IJE online).
Es ima ed in e ac ion e ec s o hese SNPs we e ex ac ed
om he me a-analysis summa y s a is ics o he ou es s
pe o med in he Hancock e al.
9
analysis: SNP-by-
smoking s a us (e e smoking s ne e smoking)
in e ac ion e ec on FEV
1
and FEV
1
/FVC; and SNP-by-
smoking pack-yea s in e ac ion e ec on FEV
1
/FVC and
FEV
1
. As shown in Supplemen a y Table 2 (a ailable as
Supplemen a y da a a IJE online), nine SNPs showed
nominal signi icance (P<0.05) ou o he 104 es s pe -
o med; howe e , none emained signi ican a e accoun -
ing o mul iple es ing (Bon e oni co ec ed P- alue
h eshold o 5 10
–4
). The minimum P- alue was obse ed
o he in e ac ion be ween s993925, nea he TGFb2
gene, and smoking s a us on FEV
1
[b
in
¼–0.036, 95%
con idence in e al (CI), –0.009 o –0.032, P¼0.007].
Nex , using hese da a, we conduc ed h ee mul i a ia e
(as opposed o single SNP) in e ac ion analyses, es ing
join ly o he in e ac ion e ec s be ween hose SNPs and
ei he smoking s a us o pack-yea s on he wo pheno ypes
(FEV
1
and FEV
1
/FVC) o a o al o 12 es s. As shown in
Table 1, none o he mul i a ia e in e ac ion es s wi h
pack-yea s was signi ican . Howe e , ou o he six mul i-
a ia e in e ac ion es s wi h smoking s a us (e e s ne e )
showed nominal signi icance, and wo es s o FEV
1
/FVC
had a P- alue below he Bon e oni signi icance le el (12
es s, P <410
–3
). The s onges signal was obse ed o
he unweigh ed gene ic isk sco e-by-smoking s a us in e -
ac ion e ec on FEV
1
/FVC (b
in
¼–0.036, 95% CI –0.040
o –0.032, P¼0.00057). The Coch an’s Q es o he e o-
genei y o he in e ac ion e ec ac oss s udies was no sig-
ni ican (P¼0.97) and he o es plo o s udy-speci ic
esul s did no display any ob ious ou lie (Supplemen a y
Figu e 1, a ailable as Supplemen a y da a a IJE online).
The con as be ween his signi ican isk sco e in e -
ac ion and he absence o s ong single SNP in e ac ion e -
ec s can be explained by looking a he dis ibu ion o he
single SNP in e ac ion e ec es ima es. Figu e 1 shows his
dis ibu ion o he alleles associa ed wi h dec eased FEV
1
/
FVC. I highligh s ha , al hough he 95% CI o mos single
SNP in e ac ion e ec s encompass he null (and he e o e
he absence o signi ican single SNP in e ac ion e ec ),
he e is an en ichmen o nega i e in e ac ion e ec s.
Indeed, e en a binomial es can be used o con i m he
unbalanced di ec ion o in e ac ion e ec s (18 o 26 in e -
ac ions a e nega i e leading o a P- alue o 0.014 o a bi-
nomial es wi h an expec ed equip obable dis ibu ion o
0.5). The gene ic isk sco e-based in e ac ion es exploi s
such en ichmen by es ing o he a e age in e ac ion e -
ec ac oss all SNPs.
14
As wi h any mul i a ia e app oach
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Table 1. Mul i a ia e in e ac ion es s o he 26 loci associa ed wi h pulmona y unc ion
Ou come Exposu e Tes ˆ
b
in
(CI) P- alue
FEV
1
Smoking s a us
a
uGRS –0.0055 (–0.011, 2.7 10
–5
)0.051
wGRS –0.21 (–0.40, –0.033) 0.020
CHISQ ––0.49
FEV
1
Pack-yea s uGRS –1.6 10
–5
(–4.6 10
–5
, 1.4 10
–5
)0.30
wGRS –6.5 10
–4
(–1.6 10
–3
, 3.3 10
–4
)0.19
CHISQ ––0.46
FEV
1
/FVC Smoking s a us uGRS –0.0099 (–0.016, –0.0043) 0.00057
b
wGRS –0.21 (–0.33, –0.073) 0.0022
b
CHISQ ––0.026
FEV
1
/FVC Pack-yea s uGRS –4.4e-06 (–3.6 10
–5
, 2.7 10
–5
)0.78
wGRS –6.5 10
–5
(–8.0 10
–4
, 6.6 10
–4
)0.85
CHISQ – – 0.53
uGRS is he gene ic isk sco e using equal weigh s o all SNPs; wGRS is he gene ic isk sco e weigh ed by e ec es ima es om he ma ginal sc eening; CHISQ
is he omnibus es o all in e ac ion e ec s; ˆ
b
in
is he es ima ed in e ac ion e ec be ween he GRS and he ou come; and CI is he con idence in e al o ha es i-
ma e. Nominally signi ican es s a e indica ed in bold.
a
Smoking s a us is de ined as ne e smoke s s e e smoke s.
b
Signi ican P- alue a e Bon e oni co ec ion.
Figu e 1. Dis ibu ion o in e ac ion e ec s on FEV
1
/FVC.
Single SNP isk allele-by-smoking s a us (e e /ne e ) in e ac ion e ec es ima es (b
in
) and 95% con idence in e als a e plo ed by inc easing alues.
The unweigh ed gene ic isk sco e-by-smoking s a us in e ac ion is plo ed a he bo om.
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based on a composi e null hypo hesis, his esul indica es
ha a leas a subse o hese 26 SNPs in e ac wi h smok-
ing s a us, bu does no allow us o de e mine which o
how many SNPs a e d i ing he gene ic isk sco e-by-
smoking in e ac ion. The h ee o he se s o single SNP
in e ac ion es s showed a simila (bu no signi ican a e
co ec ion o mul iple es ing) end wi h en ichmen o
nega i e in e ac ions (Supplemen a y Figu es 2–4, a ail-
able as Supplemen a y da a a IJE online). We summa ized
he con ibu ion o he unweigh ed gene ic isk sco e-by-
smoking in e ac ion on FEV
1
/FVC in Table 2 and
Figu e 2A. This indica es ha he dele e ious e ec o
smoking is enhanced among ca ie s o he isk alleles o
equi alen ly ha he dele e ious e ec o smoking is
educed among subjec s ca ying he p o ec i e alleles.
We used wo independen da ase s, one o 8859 un e-
la ed indi iduals and ano he o 9457 ela ed indi iduals,
o es o independen eplica ion o ou esul s
(Supplemen a y No e, a ailable as Supplemen a y da a a
IJE online). Al hough he in e ac ion e ec s we e no sig-
ni ican , bo h eplica ion samples showed consis en nega-
i e GRS-by-e e smoking in e ac ion e ec on FEV1/FVC
(^
bin ¼–0.0025, 95% CI –0.0165, 0.0115, P¼0.72 and
^
bin ¼–0.0030, 95% CI –0.0214, 0.0154, P¼0.74, and
o e all in e ac ion e ec in he combined eplica ion da a-
se s ^
bin ¼–0.0027, 95% CI –0.0136, 0.0082 P¼0.63) and
a Coch an’s Q es o he e ogenei y showed no signi ican
di e ence in he h ee e ec es ima es (P¼0.51).
To quan i y he impac o his esul om a public heal h
pe spec i e, we es ima ed he impac o he gene ic isk
sco e-by-smoking in e ac ion on ha ing FEV
1
/FVC below
1%, 5% and 20% in he lowe ails o he dis ibu ion in
he popula ion. Speci ically, we de i ed he RR o ha ing
FEV
1
/FVC below hese cu -o poin s (1%, 5% and 20%)
in e e smoke s compa ed wi h ne e smoke s. Figu e 2B
quan i ies he excess RR (i.e. he RR minus one) o indi id-
uals ac oss i e GRS quin iles. I highligh s he highe isk
associa ed wi h smoking among indi iduals ca ying isk
alleles (i.e. alleles associa ed wi h poo e pulmona y unc-
ion) as compa ed wi h indi iduals ca ying p o ec i e al-
leles (i.e. alleles associa ed wi h be e pulmona y unc ion).
Fo example, among indi iduals wi h a GRS abo e he
80 h pe cen ile, smoke s ha e on a e age a 26% excess RR
o ha ing FEV
1
/FVC in he lowes 1% o he popula ion
dis ibu ion, whe eas e e smoke s wi h a GRS below he
20 h pe cen ile ha e on a e age an 18% excess RR o all-
ing in ha same FEV
1
/FVC ca ego y compa ed wi h ne e
smoke s. Applying he same app oach o FEV
1
,we
obse ed a simila pa e n (Supplemen a y Figu e 5, a ail-
able as Supplemen a y da a a IJE online). Howe e , as
expec ed, he lowe magni ude o he gene ic isk sco e-by-
e e smoking in e ac ion on FEV
1
implied a lowe di e -
ence in RR be ween e e smoke s and ne e smoke s.
Discussion
Using he la ges da ase o da e o Eu opean ances y pa -
icipan s om he gene al popula ion wi h pulmona y
Table 2. Summa y o e ec es ima es o gene ic isk sco e-
by-smoking s a us in e ac ion on FEV
1
/FVC
P edic o s Be a SD P- alue
F om he ma ginal exposu e model
Pack-yea s –0.0030 0.00017 1.2 10
–71
Cu en smoking –0.040 0.0047 7.7 10
–18
Smoking s a us
a
–0.0023 0.0046 0.61
F om he in e ac ion model
GRS –0.0363 0.0021 3.9 10
–64
GRS Smoking s a us
a
–0.0099 0.0029 5.7 10
–4
GRS is he unweigh ed gene ic isk sco e; be a is he e ec es ima es o
each p edic o ; and SD he s anda d de ia ion o he each be a.
a
Smoking s a us was de ined as ne e smoke s s e e smoke s.
Figu e 2. O e iew o he unweigh ed gene ic isk sco e-by-smoking
in e ac ion e ec on FEV
1
/FVC.
Uppe panel (A) p esen s he dis ibu ion o he unweigh ed gene ic isk
sco e (GRS, g ey densi y plo ) and he ela ionship be ween he un-
weigh ed GRS and s anda dized FEV
1
/FVC in e e smoke s (dashed line)
and ne e smoke s (solid line). Lowe panel (B) shows he excess ela-
i e isk (RR) o ha ing FEV
1
/FVC in he lowes 1%, 5% and 20% o he
popula ion o e e smoke s compa ed wi h ne e smoke s, as s a i ied
by GRS quin iles.
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unc ion (FEV
1
/FVC and FEV
1
), smoking and gene ic da a,
we iden i ied a gene-by-smoking in e ac ion e ec on
FEV
1
/FVC by using a GRS composed o 26 SNPs iden i ied
and eplica ed in a p io GWAS me a-analysis o ma ginal
gene ic e ec s. To ou knowledge, ou s udy is he i s o
epo a syne gis ic ac ion o genes and smoking on pul-
mona y unc ion (i.e. he educ ion in FEV
1
/FVC as a e-
sul o smoking is g ea e among indi iduals who a e
gene ically p edisposed o lowe FEV
1
/FVC a io). Ou
s udy also highligh s he impo ance o de eloping and
applying al e na i e s a egies o e alua e in e ac ion e -
ec s o lung pheno ypes along wi h o he complex ai s
and diseases. The gene ic isk sco e-based app oach
enabled us o iden i y an in e ac ion when he s anda d
uni a ia e es (i.e. e alua ing each single gene ic a ian
o in e ac ion independen ly) ailed o iden i y any
in e ac ions.
Replica ion s udies showed in e ac ion e ec es ima es
in he same di ec ion as he disco e y s udy bu we e no
signi ican , and he magni ude o in e ac ion e ec s we e
subs an ially smalle . We acknowledge ha , despi e ca e ul
e alua ion o he in e ac ion e ec s in he disco e y sam-
ple, he obse ed signal migh be o e es ima ed o con-
ounded by unmeasu ed complex ac o s. Howe e , we
can a p io i ule ou a sys ema ic bias o he single SNP
in e ac ion e ec s in he disco e y s udy, because he gen-
omic in la ion ac o k, de ined as he a io o he median
o he empi ically obse ed dis ibu ion o he es s a is ic
o he expec ed median,
30
was no subs an ially di e en
om 1 (k¼1.044 o FEV1/FVC and smoking s a us).
Ins ead, di e ences in signi icance and e ec es ima es
migh be pa ly explained by he limi ed sample size in he
eplica ion s udy and di e ences in he analy ical design.
Indeed, he disco e y analysis was pe o med using a sa u-
a ed model including h ee smoking exposu es and expli-
ci ly modelled he in e ac ion e ec . In compa ison, he
eplica ion analysis was no adjus ed o cu en smoking
s a us and pack-yea , and he in e ac ion e ec was
app oxima ed om analyses s a i ied by smoking s a us
ou come, which has some limi a ions (see Supplemen a y
No e and Supplemen a y Figu e 6, a ailable as
Supplemen a y da a a IJE online). P e ious wo k has
shown ha combined analyses a e mo e powe ul when e -
ec s exis in bo h s a a,
31
as obse ed in disco e y s udy.
Fu he , e en wi h N¼18 316 indi iduals in he combined
eplica ion popula ion, we a e unde powe ed. This sample
size p o ides less han 50% powe , a nominal signi icance
o 5%, o de ec in e ac ion e ec s wi h he GRS.
Gene ic isk sco e-by-exposu e in e ac ion can ha e
highe clinical alue han he iden i ica ion o single SNP-
by-exposu e in e ac ion by cap u ing a weal h o in o ma-
ion in a single measu e o iden i y subg oups in he
popula ion whose gene ic backg ound makes hem mo e
suscep ible o he dele e ious e ec s o smoking.
19,32,33
Indeed, i single SNP-by-smoking in e ac ions a e dis ib-
u ed uncondi ionally on he ma ginal gene ic e ec (i.e.
in e ac ion e ec s a e equally likely o be posi i e o nega-
i e gi en ha he coded alleles a e he isk alleles), he
gene ic e ec is expec ed o be simila be ween e e and
ne e smoke s. The en ichmen o nega i e in e ac ions
we iden i ied h ough ou GRS app oach e eals a s onge
gene ic componen among he e e smoke subg oup in he
popula ion and can allow he implemen a ion o mo e e i-
cien implemen a ion o p e en ion s a egies. Fo ex-
ample, in he public heal h se ing, p og ammes a ge ing
smoking cessa ion campaigns o indi iduals who a e gene -
ically p edisposed o low pulmona y unc ion may ha e a
s onge impac in p e en ing COPD.
Ou esul s may also elucida e biological mechanisms
unde lying he in e play be ween genes and smoking in
pulmona y unc ion. In pa icula , he highe s a is ical
powe o he gene ic isk sco e-based in e ac ion es
poin s owa ds he po en ial p esence o an unmeasu ed
in e media e bioma ke media ing he e ec o he 26 loci
on FEV
1
/FVC. As shown in Figu e 3, he mos pa simoni-
ous model (i.e. he less complex ollowing Occam’s azo )
ha would explain mul iple in e ac ions going in he same
di ec ion (Figu e 1) implies ha he gene ic a ian s
Figu e 3. Unde lying causal model.
Po en ial causal diag ams unde lying he gene and smoking in e ac ion
e ec s on FEV
1
/FVC. Panel (A) p esen s a scena io whe e each gene ic
a ian in luences he ou come h ough a SNP-speci ic pa hway, and
in e ac ions wi h he en i onmen al exposu e ake place along hese
pa hways. Panel (B) p esen s an al e na i e (and simple ) model whe e
mul iple gene ic a ian s in luence an unmeasu ed in e media e bio-
ma ke U, which e ec on FEV
1
/FVC depends on smoking. In scena io
(A), he single SNP-by-smoking in e ac ion es is he op imal app oach,
whe eas, in scena io (B), he single SNP-by-smoking in e ac ion es
can become ine icien , and in e ac ion would be easie o de ec using
a gene ic isk sco e-by-smoking in e ac ion es , because i summa izes
all in e ac ion e ec s in a single es .
902 In e na ional Jou nal o Epidemiology, 2017, Vol. 46, No. 3
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