lp/j pl/jkk/hlj p h a r m a c o g e n e t i c a n a l y s i s o f t h e c a r d i o v a s c u l a r...
TRANSCRIPT
LP/J
PL/JKK/HlJ
P H A R M A C O G E N E T I C A N A L Y S I S O F T H E
C A R D I O V A S C U L A R R E S P O N S E
I N I N B R E D M I C E
• Internal Medicine Thierry Pedrazzini
• Medical GeneticsCorinne Berthonneche, Fanny Schüpfer, Fabienne Maurer, Bastian Peter, Micha Hersch, Sven Bergmann, Jacqui Beckmann
• Pharmacology and Cardiology / DKF UNIBE Hugues Abriel
• Computer Science and Engineering Eleazar Eskin (UCLA)
• atenolol (β-adrenergic receptor blocker)
• isoproterenol (β-adrenergic receptor agonist)
P R O J E C T
SBP : Systolic Blood PressureHR : Heart Rate
euthanasy
tissues plasma
days
or ISOPROTERENOL
or ATENOLOL
0 7 14
SBP and HR recording training phase
SBPHR
ECG urin
e
CONTROL
osmotic mini-pump implantation for continuous and controlled drug delivery
n=10 mice per condition and per strain
P R O T O C O L
n=10 mice per condition and per strain
23 strains
total > 1000 mice
iso high doseiso low doseatenololcontrol
strain 1
strain 2
… strain n
P R O T O C O L
phenotypes measured in conscious mice
HR (TC) heart rate (tail-cuff; beats/min)SBP systolic blood pressure (tail-cuff; mmHg)BWS body weight at start (g)BWE body weight at end (g)BWG body weight gain (g)
ECG values measured in anaesthesised mice
HR (ECG) heart rate (beats/min)Pamp amplitude of p wave (mV)Parea area of p wave (mV*ms)Pdur duration of p wave (ms)PR PR interval (ms)RR RR interval (ms)Qamp amplitude of Q wave (mV)QRS QRS interval (ms)QRSarea area of QRS complex (mV*ms)QT QT interval (ms)QTc corrected QT interval (ms)Ramp amplitude of R wave (mV)Samp amplitude of S wave (mV)ST ST interval (ms)
phenotypes measured in euthanised mice
HW heart weight at end (mg)VW weight of cardiac ventricles (mg)VWI ventricular weight index (ratio VW/BWE in mg/g)VW/BWS ventricular weight index (ratio VW/BWS in mg/g)AW weight of cardiac atria (mg)AWI atrial weight index (ratio AW/BWE in mg/g)AW/BWS atrial weight index (ratio AW/BWS in mg/g)VW/AW ratio VW/AW
P H E N O T Y P E S
• all phenotypes and responses to drug treatments are highly heritable (h2>0.7)
• ctr measurements are consistent with data from other studies
• responses to drug exposure are trait-, drug-, and dose-specific
• responses are significantly more pronounced under β-stimulation than β-blockade
• there is compartmental and strain-specific cardiac sensitivity to iso, with atria responding at lower concentrations than ventricles in the majority of the strains
• there is little concordance between strain similarity based on the phenotypes and genotypic relatedness computed from genomic SNP profiles.
« cardiovascular phenotypes are unlikely to segregate according to global phylogeny, but rather be governed by smaller, local differences in the genetic architecture of the various strains »
P H E N O T Y P E S - S U M M A R Y
• all phenotypes and responses to drug treatments are highly heritable (h2>0.7)
• ctr measurements are consistent with data from other studies
• responses to drug exposure are trait-, drug-, and dose-specific
• responses are significantly more pronounced under β-stimulation than β-blockade
• there is compartmental and strain-specific cardiac sensitivity to iso, with atria responding at lower concentrations than ventricles in the majority of the strains
• there is little concordance between strain similarity based on the phenotypes and genotypic relatedness computed from genomic SNP profiles.
cardiovascular phenotypes are unlikely to segregate according to global phylogeny, but rather be governed by smaller, local differences in the genetic architecture of the various strains
P H E N O T Y P E S - S U M M A R Y
ECG
heart rate
systolic blood pressure
non invasive measurement
s
tissues
• heart
• liver
transcriptional
analyses proteomics
etc...
plasma; urine
pharmacokinetics
(+ metabolites)
1 mouse
P R O T O C O L
microarrays
RNA-seq
G W A s
Efficient mixed-model association (EMMA) corrects for population structure and genetic relatedness in model organism association mapping
BWt-test
chromosomes
pointwise -log10 p-values -> 6000 SNPs at p≤10–6 and 283 SNPs with p<10–10
38 strains
ca 100’000 SNPs
BWt-test
BWEMMA
“ Although the strongest signals for the body weight after applying the mixed model are not genome-wide significant, they are concentrated in a region around 114 Mb in chromosome 8. This region almost exactly falls into the LOD peak of a previously known body weight QTL Bwq3. ”
p=3.8x10-6
explains 39% of the genetic variance component
BWt-test
38 strains
BWEMMA
LWt-test
34 strains
LWEMMA
p=3.8x10-6
explains 39% of the genetic variance component
p=1.2x10-9
explains 59% of the genetic variance component
G E N O M E - W I D E A S S O C I A T I O N
• 18 phenotypes
• 4 conditions (ctr, ate, iso1, iso10 )
• 88’263 SNPs across 22 strains ( Broad1 SNP dataset !)
• 2 statistical tests (REMLt and LRT)
• -> 144 scans
G W A S C A N S F O R
V W I
A N I L L U S T R A T I O N O F E M M A R E S U L T S
I S O P R O T E R E N O L - I N D U C E D C A R D I A C H Y P E R T R O P H Y
adapted from: Zarrinpashneh et al. AMPKα2 counteracts the development of cardiac hypertrophy induced by isoproterenol. BBRC 376:677-681, 2008
PW posterior wall thicknessMCSA mean cardiac myocyte
cross-sectional area
Mice challenged by daily IP injections of 50 mg/kg isoproterenol for
1 wk
R E S U L T SVWI (ratio VW/BWE)
ate
iso1
iso10
ctr
REMLt
1 2 X19
1817
1615
1413
1211
1098765430
4
2
0
4
6
8
2
0
4
6
8
2
0
4
6
8
2
LRT
1 2 X19
1817
1615
1413
1211
109876543 0
4
6
8
2
0
4
6
8
2
0
4
6
8
2
0
4
6
8
2
32 « loci »with
unadjusted p < 10-5
T O P 1 0 0 0 H I T S
1 2 3 4
5 6 7 8
9 10 11 12
13 14 15 16
chr3 81-85 Mb / ctr REMLt chr3 86-90 Mb / ctr REMLt chr4 94.8 Mb / iso1 REMLt chr7 75-77 Mb / ate REMLt
chr1 11.5-12.5 Mb / ate LRT chr1 38.5-39.5 Mb / ate LRT chr2 130-132 Mb / ate LRT chr2 117-118 Mb / iso1 REMLt
chr4 151-153 Mb / iso10 REMLt chr10 110-111 Mb / iso1 REMLtchr1 94.5-95.5 Mb / iso10 REMLt chr2 119-121 Mb / iso10 REMLt
chr5 104-105 Mb / iso10 REMLt chr6 76-77 Mb / iso10 LRT chr5 127-129 Mb / ate REMLt chr9 65-66 Mb / ate REMLt
10
8
6
4
2
0
17 18 19 20
21 22 23 24
25 26 27 28
29 30 31 32
chr7 16-17 Mb / iso1 REMLt chr6 125-126 Mb / iso1 REMLt chr7 24.5-25.5 Mb / iso1 REMLt chr4 72-73.5 Mb / iso10 REMLt
chr4 82.5-83.5 Mb / iso10 REMLtchr6 145-146 Mb / iso10 REMLt chr6 5-6 Mb / iso10 REMLt chr18 60.5-61.5 Mb / iso10 LRT
chr4 135-136 Mb / ctr LRT chr5 45-46 Mb / iso1 LRT chr5 47-48 Mb / iso1 LRT chr12 101-103 Mb / iso10 LRT
chr12 113-114 Mb / iso10 LRT chr6 110-111 Mb / iso10 LRT chr1 3-3.5 Mb / iso10 REMLt chr17 12-13 Mb / iso10 REMLt
10
8
6
4
2
0
Q U A L I T Y C H E C K
32 loci for VWI (across 4 conditions and 2 statistical tests)
1. check whether p-values were obtained at positions with full allele sets across the 22 strains
- if yes, check SDP and consistency of results across statistical tests
- if not, try to extrapolate a « corrected p-value » from a nearby SNP with a similar SDP and a full allele set (using the publicly available Broad1 and/or the imputed CGD1 SNP datasets)
2. list putative candidate genes (UCSC genome browser, biblio, etc…)
E X A M P L E 1 Q U A L I T Y C H E C K
ate
iso1
iso10
ctr
1 2 X19
1817
1615
1413
1211
1098765430
4
2
0
4
6
8
2
0
4
6
8
2
0
4
6
8
2
REMLt
1 2 X19
1817
1615
1413
1211
109876543 0
4
6
8
2
0
4
6
8
2
0
4
6
8
2
0
4
6
8
2
LRT
E X A M P L E 1 Q U A L I T Y C H E C K
Locus 18Significance (based on data with full allele set): CORRECT
Top hit: position chr 6:125'528'422alleles (EMMA) # alleles 1 = 17; # alleles 2 = 5 condition / stat iso1, REMLTp-value: 4.07x10-6
unadjusted p-values across conditions
ctr REMLt ate REMLt iso1 REMLt iso10 REMLt ctr LRT ate LRT iso1 LRT iso10 LRT6.2x10-5 3.7x10-5 4.07x10-6 2.67x10-5 2.77x10-4 2.04x10-4 5.62x10-5 1.63x10-4
0
4
6
2-log
10 p
EM
MA
E X A M P L E 1 Q U A L I T Y C H E C K
Locus 18Significance (based on data with full allele set): CORRECT
Top hit: position chr 6:125'528'422alleles (EMMA) # alleles 1 = 17; # alleles 2 = 5 condition / stat iso1, REMLTp-value: 4.07x10-6
C3
H-H
eJ
C3
H-H
eO
uJ
KK
-HlJ
SJL
-JA
-JC
BA
-JN
OD
-Sh
iLtJ
C5
7B
L-6
J_C
RL
C5
8-J
FV
B-N
JS
WR
-JC
57
BL
KS
-JB
TB
Rtp
lust
f-J
Ba
lb-c
JL
P-J
AK
R-J
C5
7B
L-6
Jax
I-L
nJ
NZ
B-B
lNJ
Ba
lb-c
ByJ
DB
A-2
JS
M-J
12
9S
1-S
vIm
JP
L-J
2.5
3.5
4.5
5.5
6.5
7.5
8.5
VW
I
G G G G G G G G G G G GG G G GA A A A AGGvWF intron 6
Ranking strains by increasing VWI means in the iso1 group:
0
4
6
2
vWF intron 6
window: 124-126 Mb
E X A M P L E 2 Q U A L I T Y C H E C K
ate
iso1
iso10
ctrREMLt
1 2 X19
1817
1615
1413
1211
1098765430
4
2
0
4
6
8
2
0
4
6
8
2
0
4
6
8
2
LRT
1 2 X19
1817
1615
1413
1211
109876543 0
4
6
8
2
0
4
6
8
2
0
4
6
8
2
0
4
6
8
2
E X A M P L E 2 Q U A L I T Y C H E C K
Locus 9Significance (based on data with full allele set): INFLATED (but p-values still below 10-5)
Top hit 1 : position chr 4:151'355'820alleles (EMMA) # alleles 1 = 16; # alleles 2 = 5condition / stat iso1, REMLtp-value: 3.35x10-7
Top hit 2 : position chr 4:152'394'133alleles (EMMA) # alleles 1 = 17; # alleles 2 = 4condition / stat iso10, REMLtp-value: 2.31x10-7
E X A M P L E 2 Q U A L I T Y C H E C K
unadjusted p-values across conditionsposition #1 #2 ctr R ate R iso1 R iso10 R ctr L ate L iso1 L iso10 L
151'355'820 16 5 2.06x10-5 7.62x10-5 3.35x10-7 5.8x10-6 1.29x10-4 3.06x10-4 1.39x10-5 6.05x10-5
152'394'133 17 4 3.13x10-5 2.48x10-4 4x10-7 2.31x10-7 1.66x10-4 6.75x10-4 1.52x10-5 9.93x10-6
0
4
6
2-l
og
10 p
EM
MA
0
4
6
2
-log
10 p
EM
MA
iso1
iso10
151'352'086 16 6 7.31x10-5 2.85x10-4 2.87x10-6 6.66x10-5 3.02x10-4 7.65x10-4 4.57x10-5
2.74x10-4
152'341'831 17 5 1.17x10-4 8.58x10-4 4.15x10-6 8.03x10-6 4.09x10-4 1.67x10-3 5.59x10-5 7x10-5
E X A M P L E 2 Q U A L I T Y C H E C K
C3
H-H
eJ
C3
H-H
eO
uJ
SJL
-JC
BA
-JC
57
BL
-6Ja
xB
alb
-cJ
FV
B-N
JC
58
-JN
OD
-Sh
iLtJ
AK
R-J
SW
R-J
C5
7B
LK
S-J
C5
7B
L-6
J_C
RL
A-J
BT
BR
tplu
stf-
JN
ZB
-BlN
JK
K-H
lJI-
Ln
JL
P-J
Ba
lb-c
ByJ
SM
-JD
BA
-2J
PL
-J1
29
S1
-SvI
mJ
2.5
3.5
4.5
5.5
6.5
7.5
8.5
VW
I
C3
H-H
eJ
C3
H-H
eO
uJ
KK
-HlJ
SJL
-JA
-JC
BA
-JN
OD
-Sh
iLtJ
C5
7B
L-6
J_C
RL
C5
8-J
FV
B-N
JS
WR
-JC
57
BL
KS
-JB
TB
Rtp
lust
f-J
Ba
lb-c
JL
P-J
AK
R-J
C5
7B
L-6
Jax
I-L
nJ
NZ
B-B
lNJ
Ba
lb-c
ByJ
DB
A-2
JS
M-J
12
9S
1-S
vIm
JP
L-J
2.5
3.5
4.5
5.5
6.5
7.5
8.5
VW
I
iso1 iso10
chr 4:151'355'820
unadjusted p-values across conditionsposition #1 #2 ctr R ate R iso1 R iso10 R ctr L ate L iso1 L iso10 L
151'355'820 16 5 2.06x10-5 7.62x10-5 3.35x10-7 5.8x10-6 1.29x10-4 3.06x10-4 1.39x10-5 6.05x10-5
152'394'133 17 4 3.13x10-5 2.48x10-4 4x10-7 2.31x10-7 1.66x10-4 6.75x10-4 1.52x10-5 9.93x10-6
T T T T T T T T T T T T T T G TT G G G GT
chr 4:152'394'133
C C C C C C C C C C C C C C T TC C C T TC
151'352'086 16 6 7.31x10-5 2.85x10-4 2.87x10-6 6.66x10-5 3.02x10-4 7.65x10-4 4.57x10-5
2.74x10-4
152'341'831 17 5 1.17x10-4 8.58x10-4 4.15x10-6 8.03x10-6 4.09x10-4 1.67x10-3 5.59x10-5 7x10-5
chr 4:151'352'086
T T T T T T T T T T T T T T C TT C C C CT G GGG GG GG G GG G GG T TG G G T TG
chr 4:152'341'831
E X A M P L E 2 Q U A L I T Y C H E C K
window: 151-153.5 Mb
very little information on these• Dnajc11 [Hsp40] and Thap3 « interact with Acetaminophen »
• Phf13: PHD finger protein
• Klhl21: probable substrate-specific adapter of an E3 ubiquitin- protein ligase complex (by similarity); may be expressed in the heart (mouse arrays)
E X A M P L E 3 Q U A L I T Y C H E C K
ate
iso1
iso10
ctrREMLt
1 2 X19
1817
1615
1413
1211
1098765430
4
2
0
4
6
8
2
0
4
6
8
2
0
4
6
8
2
LRT
1 2 X19
1817
1615
1413
1211
109876543 0
4
6
8
2
0
4
6
8
2
0
4
6
8
2
0
4
6
8
2
E X A M P L E 3 Q U A L I T Y C H E C K
0
4
6
2-log
10 p
EM
MA
Locus 10Significance (based on data with full allele set): INFLATED
Top hit : position chr 10:110'702'509alleles (EMMA) # alleles 1 = 16; # alleles 2 = 4condition / stat iso1, REMLtp-value: 1.588x10-6
unadjusted p-values across conditionsposition #1 #2 ctr R ate R iso1 R iso10 R ctr L ate L iso1 L iso10 L
110'702'509 16 4 7.55x10-6 2.38x10-5 1.59x10-6 4.2x10-6 1.01x10-4 1.91x10-4 4.16x10-5
6.97x10-5
110'607'856 18 4 2.06x10-5 6.22x10-5 1.14x10-5 3.76x10-4 1.58x10-4 3.02x10-4 1.05x10-4
9.53x10-4
E X A M P L E 3 Q U A L I T Y C H E C K
C3
H-H
eJ
C3
H-H
eO
uJ
KK
-HlJ
SJL
-JA
-JC
BA
-JN
OD
-Sh
iLtJ
C5
7B
L-6
J_C
RL
C5
8-J
FV
B-N
JS
WR
-JC
57
BL
KS
-JB
TB
Rtp
lust
f-J
Ba
lb-c
JL
P-J
AK
R-J
C5
7B
L-6
Jax
I-L
nJ
NZ
B-B
lNJ
Ba
lb-c
ByJ
DB
A-2
JS
M-J
12
9S
1-S
vIm
JP
L-J
2.5
3.5
4.5
5.5
6.5
7.5
8.5
VW
I
iso1
chr 10:110'702'509 T T T T T T T T T T T T T T T CT C C C CT
unadjusted p-values across conditionsposition #1 #2 ctr R ate R iso1 R iso10 R ctr L ate L iso1 L iso10 L
110'702'509 16 4 7.55x10-6 2.38x10-5 1.59x10-6 4.2x10-6 1.01x10-4 1.91x10-4 4.16x10-5
6.97x10-5
110'607'856 18 4 2.06x10-5 6.22x10-5 1.14x10-5 3.76x10-4 1.58x10-4 3.02x10-4 1.05x10-4
9.53x10-4
T T T T T T T T T T T T T T T GT G G T GTC C C C C C C C C C C C C C C TC T C C TCG GGGGGGGGGGG G G G AG A GG AGC C C C C C C C C C C C C C C AC A A C ACG GGGGGGGGGGG G G G AG A GG AGC C C C C C C C C C C C C C C CC C A C CCG GGGGGGGGGGG G G G CG C C GGG
chr 10:110'607'856
chr 10:110'636'818
E X A M P L E 3 Q U A L I T Y C H E C K
window: 110-111 Mb
Osbpl8 : oxysterol-binding protein-like protein 8 isoform . . .
NATURE GENETICS VOLUME 40 NUMBER 5 MAY 2008 546
Integrated genomic appraoches implicate osteoglycin (Ogn) in the regulation of left ventricular mass
Enrico Petretto1,2,11, Rizwan Sarwar1,11, Ian Grieve1, Han Lu1, Mande K Kumaran1, Phillip J Muckett1, Jonathan Mangion1, Blanche Schroen1, Matthew Benson1, Prakash P Punjabi3, Sanjay K Prasad3, Dudley J Pennell3, Chris Kiesewetter3, Elena S Tasheva4, Lolita M Corpuz4, Megan D Webb4, Gary W Conrad4, Theodore W Kurtz5, Vladimir Kren6,7, Judith Fischer8, Norbert Hubner8, Yigal M Pinto9, Michal Pravenec6,7, Timothy J Aitman1,10 & Stuart A Cook1,3
1Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK. 2Division of Epidemiology, Public Health and Primary Care, Faculty of Medicine, Imperial College, Praed Street, London, W2 1PG, UK. 3National Heart and Lung
Institute, Imperial College, Dovehouse Street, London, SW3 6LY, UK. 4Division of Biology, 116 Ackert Hall, Kansas State University, Manhattan, Kansas 66506-4901,
USA. 5Department of Laboratory Medicine, University of California, San Francisco, California 94143-0134, USA. 6Institute of Physiology, Czech Academy of Sciences
and Centre for Applied Genomics, Vídeská 1083, 142 20 Prague 4, Czech Republic. 7Charles University in Prague, Institute of Biology and Medical Genetics of the First
Faculty of Medicine and General Teaching Hospital, Albertov 4, 128 00 Prague 2, Czech Republic. 8Max-Delbrück Center for Molecular Medicine, Robert-Rössle-
Strasse 10, Berlin-Buch, 13125, Germany. 9Heart Failure Research Center, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands. 10Section of Molecular Genetics and Rheumatology, Division and Faculty of Medicine, Imperial College, Hammersmith Hospital, Du Cane Road, London, W12 0NN. 11These authors contributed equally to this work. Correspondence to: Timothy J Aitman1,10 ([email protected]) or Stuart A Cook1,3 ([email protected] )
34
1
ctriso10
E X A M P L E 4 Q U A L I T Y C H E C K
ate
iso1
iso10
ctrREMLt
1 2 X19
1817
1615
1413
1211
1098765430
4
2
0
4
6
8
2
0
4
6
8
2
0
4
6
8
2
LRT
1 2 X19
1817
1615
1413
1211
109876543 0
4
6
8
2
0
4
6
8
2
0
4
6
8
2
0
4
6
8
2
E X A M P L E 4 Q U A L I T Y C H E C K
Locus 13Significance (based on data with full allele set): INFLATED ?
Top hit 1 : position chr 5:104'572'764alleles (EMMA) # alleles 1 = 15; # alleles 2 = 5condition / stat iso10, REMLtp-value: 8.03x10-7
Top hit 2 : position chr 5:104'515'280alleles (EMMA) #alleles 1 = 17; # alleles 2 = 4condition / stat iso10, REMLtp-value: 5.597x10-6
E X A M P L E 4 Q U A L I T Y C H E C K
0
4
6
2-l
og
10 p
EM
MA
iso10
unadjusted p-values across conditionsposition #1 #2 ctr R ate R iso1 R iso10 R ctr L ate L iso1 L iso10 L
104'572'764 15 5 3.65x10-4 5.52x10-4 1.64x10-5 8.03x10-7 1.09x10-3 1.38x10-3 1.56x10-4
4.08x10-5
104'515'280 17 4 1.3x10-3 1.14x10-3 9.77x10-5 5.6x10-6 2.52x10-3 2.21x10-3 4.12x10-4 9.5x10-5
E X A M P L E 4 Q U A L I T Y C H E C K
unadjusted p-values across conditionsposition #1 #2 ctr R ate R iso1 R iso10 R ctr L ate L iso1 L iso10 L
104'572'764 15 5 3.65x10-4 5.52x10-4 1.64x10-5 8.03x10-7 1.09x10-3 1.38x10-3 1.56x10-4
4.08x10-5
C3
H-H
eJ
C3
H-H
eO
uJ
SJL
-JC
BA
-JC
57
BL
-6Ja
xB
alb
-cJ
FV
B-N
JC
58
-JN
OD
-Sh
iLtJ
AK
R-J
SW
R-J
C5
7B
LK
S-J
C5
7B
L-6
J_C
RL
A-J
BT
BR
tplu
stf-
JN
ZB
-BlN
JK
K-H
lJI-
Ln
JL
P-J
Ba
lb-c
ByJ
SM
-JD
BA
-2J
PL
-J1
29
S1
-SvI
mJ
2.5
3.5
4.5
5.5
6.5
7.5
8.5
VW
I
chr 5:104‘572‘764 C C C C C C C C C C C C C C C TC T T T TC
chr 5:104‘515‘280 C C C C C C C C C C C C C C CC T T T TC
iso10
104'515'280 17 4 1.3x10-3 1.14x10-3 9.77x10-5 5.6x10-6 2.52x10-3 2.21x10-3 4.12x10-4 9.5x10-5
E X A M P L E 4 Q U A L I T Y C H E C K
window: 104-105 Mb
Sparcl1 : Protein of the ECM. SPARC-like protein 1, a member of the SPARC family, is downregulated in various tumours. Information is otherwise sparse.BUT : the analogue Sparc (osteonectin) was identified as a cis-eQTL associated with indexed cardiac mass in the rat. There is further experimental evidence for a link between Sparc and cardiac hypertrophy.
NATURE GENETICS VOLUME 40 NUMBER 5 MAY 2008 546
Integrated genomic appraoches implicate osteoglycin (Ogn) in the regulation of left ventricular mass
Enrico Petretto1,2,11, Rizwan Sarwar1,11, Ian Grieve1, Han Lu1, Mande K Kumaran1, Phillip J Muckett1, Jonathan Mangion1, Blanche Schroen1, Matthew Benson1, Prakash P Punjabi3, Sanjay K Prasad3, Dudley J Pennell3, Chris Kiesewetter3, Elena S Tasheva4, Lolita M Corpuz4, Megan D Webb4, Gary W Conrad4, Theodore W Kurtz5, Vladimir Kren6,7, Judith Fischer8, Norbert Hubner8, Yigal M Pinto9, Michal Pravenec6,7, Timothy J Aitman1,10 & Stuart A Cook1,3
1Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK. 2Division of Epidemiology, Public Health and Primary Care, Faculty of Medicine, Imperial College, Praed Street, London, W2 1PG, UK. 3National Heart and Lung
Institute, Imperial College, Dovehouse Street, London, SW3 6LY, UK. 4Division of Biology, 116 Ackert Hall, Kansas State University, Manhattan, Kansas 66506-4901,
USA. 5Department of Laboratory Medicine, University of California, San Francisco, California 94143-0134, USA. 6Institute of Physiology, Czech Academy of Sciences
and Centre for Applied Genomics, Vídeská 1083, 142 20 Prague 4, Czech Republic. 7Charles University in Prague, Institute of Biology and Medical Genetics of the First
Faculty of Medicine and General Teaching Hospital, Albertov 4, 128 00 Prague 2, Czech Republic. 8Max-Delbrück Center for Molecular Medicine, Robert-Rössle-
Strasse 10, Berlin-Buch, 13125, Germany. 9Heart Failure Research Center, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands. 10Section of Molecular Genetics and Rheumatology, Division and Faculty of Medicine, Imperial College, Hammersmith Hospital, Du Cane Road, London, W12 0NN. 11These authors contributed equally to this work. Correspondence to: Timothy J Aitman1,10 ([email protected]) or Stuart A Cook1,3 ([email protected] )
Supplementary Table 2. Cis-eQTLs detected with FDR ≤ 5%, an absolute fold change > 1.5 at the peak of linkage by parental genotype, and that co-localize with cardiac mass QTLs (i.e., between genetic markers at the extremes of the QTL region as defined in the Rat Genome Database, http://rgd.mcw.edu/) that have been mapped in the SHR or BN strain crosses.
Probeset Id Gene Symbol Chr PGW FDR (%) LOD score Fold change
1367562_at Sparc* 10 8.5x10-5 0.6% 7.0 1.6
1376749_at Ogn 17 1.7x10-3 4.1% 6.0 2.7 1383263_at Ogn 17 1.3x10-3 3.2% 6.3 2.5
1368574_at Adra1b◊* 10 1.0x10-6 0.4% 10.2 1.8
1398844_at Txn2 ◊ 7 6.6x10-5 0.5% 7.6 -1.6
* these genes are located in the same QTL in the rat◊ these genes are major determinants of cardiac hypertrophy in the mouse
There are 76 entries (70 genes) in the original table
NATURE GENETICS VOLUME 40 NUMBER 5 MAY 2008 546
ctriso10
S U M M A R Y Q U A L I T Y C H E C K
Of the 32 loci for VWI with pEMMA<10-5 :
• 16 loci based on SNP(s) with full allele sets across the 22 strains
- 11 judged as « correct » (p-values are consistent across tests); these hits fall mainly in gene-poor regions
- 5 judged as « false positives » (inconsistent data)
• 16 loci based on SNP(s) with incomplete allele sets across the 22 strains
- at least 10 have inflated p-values
• Candidate genes ?
1 2 3 4
5 6 7 8
9 10 11 12
13 14 15 16
chr3 81-85 Mb / ctr REMLt chr3 86-90 Mb / ctr REMLt chr4 94.8 Mb / iso1 REMLt chr7 75-77 Mb / ate REMLt
chr1 11.5-12.5 Mb / ate LRT chr1 38.5-39.5 Mb / ate LRT chr2 130-132 Mb / ate LRT chr2 117-118 Mb / iso1 REMLt
chr4 151-153 Mb / iso10 REMLt chr10 110-111 Mb / iso1 REMLtchr1 94.5-95.5 Mb / iso10 REMLt chr2 119-121 Mb / iso10 REMLt
chr5 104-105 Mb / iso10 REMLt chr6 76-77 Mb / iso10 LRT chr5 127-129 Mb / ate REMLt chr9 65-66 Mb / ate REMLt
10
8
6
4
2
0
CORRECT
INFLATED
CORRECT
CORRECT
INFLATED
INFLATED ?
CORRECT
INFLATED
INFLATED but o
k
INFLATED
INFLATED
INFLATED ?
INFLATED ?
CORRECT
CORRECT
CORRECT
17 18 19 20
21 22 23 24
25 26 27 28
29 30 31 32
chr7 16-17 Mb / iso1 REMLt chr6 125-126 Mb / iso1 REMLt chr7 24.5-25.5 Mb / iso1 REMLt chr4 72-73.5 Mb / iso10 REMLt
chr4 82.5-83.5 Mb / iso10 REMLtchr6 145-146 Mb / iso10 REMLt chr6 5-6 Mb / iso10 REMLt chr18 60.5-61.5 Mb / iso10 LRT
chr4 135-136 Mb / ctr LRT chr5 45-46 Mb / iso1 LRT chr5 47-48 Mb / iso1 LRT chr12 101-103 Mb / iso10 LRT
chr12 113-114 Mb / iso10 LRT chr6 110-111 Mb / iso10 LRT chr1 3-3.5 Mb / iso10 REMLt chr17 12-13 Mb / iso10 REMLt
10
8
6
4
2
0
INFLATED ?
CORRECT
CORRECT
INFLATED but o
k
INFLATED ?
CORRECT
INFLATED
INFLATED ?
CORRECT
FALSE POSITIVE
FALSE POSITIVE
INFLATED
INFLATED
FALSE POSITIVE
FALSE POSITIVE
FALSE POSITIVE
I N S U M M A R Y
Issues
• POWER
• Genome-wide significance ?
• Perform QC across all scans
• Prioritize candidate genes
N O T E S
location 128(Build 37) SNP
annotation
19 56.794902 Adrb1 L G G G G g G G G g g g G G g G g G g g g g19 56.794953 Adrb1 L G G G G g G G G g g g G G g G g G g g g g19 56.795034 Adrb1 L A A A A a A A A a a a A A a A a A a a a a19 56.795054 Adrb1 L G G G G g G G G g g g G G g G g G g g g g19 56.795157 Adrb1 L T T T T t T T T t t t T T t T t T t t t t19 56.795285 Adrb1 L G G G G g G G G g g g G G g G g G g g g g19 56.795406 Adrb1 L C C C C c C C C c c c C C c C c C c c c c19 56.795650 Adrb1 L T t t T t t T T t t t T T t T t T t t t t19 56.795907 Adrb1 L G g g G g g G G g g g G G g g g G g g g g19 56.795922 Adrb1 L A a a A a a A A a a a A A a A a A a a a a
129S
1/Sv
ImJ
A/J
AKR/J
BALB
/cByJ
BALB
/cJ
BTBR T
+ tf/
J
C3H
/HeJ
C57
BL/
6J
C57
BLK
S/J
C58
/J
CBA/J
DBA/2
J
FVB/N
J
I/Ln
J
KK/H
lJ
LP/J
NO
D/S
hiLt
J
NZB
/BlN
J
PL/J
SJL/
J
SM/J
SWR/J
SDP in Adrb1 in the CV-PGX panel
Source: CGD1 imputed SNP panel (MPD)
« L O C I » W I T H p <10-5
AWI 8 loci (p min = 4.93x10-8) VWI 32 loci (p min = 2.31x10-7) BWE 12 loci (p min = 3.81x10-8)
R L R L R L R L R L R L R L R L R L R L R L R L
C R 3 1 1 1 1 C R 5 2 3 1 C R 8 1 6 6 1 4 2
L 1 1 L 1 L 1 1 1 1 1 1 1
A R 1 4 1 1 A R 2 4 2 A R 6 1 6 5 1 4 2
L 1 1 1 L 3 1 L 1
I1 R 1 1 2 I1 R 3 2 8 1 4 1 I1 R 6 1 5 8 1 5 2
L 0 L 1 3 1 L 1 1 1 1 1 1 1
I10 R 1 I10 R 1 1 4 1 13 I10 R 4 1 4 5 1 6 2
L 0 L 1 8 L 2 1 2 2 1 2 2
HR 9 loci (p min = 1.89x10-8) SBP 12 loci (p min = 3.67x10-9) BWG 16 loci (p min = 5.82x10-12)
R L R L R L R L R L R L R L R L R L R L R L R L
C R 0 C R 3 1 2 1 1 1 1 C R 9 5
L 0 L 1 1 1 1 1 L 5 5
A R 5 1 A R 2 1 7 2 2 1 1 A R 3 2
L 1 1 L 1 2 2 1 1 L 2 2
I1 R 0 I1 R 1 1 2 1 3 2 I1 R 0
L 0 L 1 1 1 2 2 L 0
I10 R 4 1 I10 R 1 1 1 4 1 I10 R 4 2
L 1 1 L 1 1 L 2 2
C A I1 I10 A I1 I10C I1 I10C A
I1 I10C A I1 I10 C A I10C A I1
AWI VWI BWS BWE BWG HR SBP
R L R L R L R L R L R L R L R L R L R L R L R L R L R L R L R L R L R L R L R L R L R L R L R L R L R L R L R L
AWI R 3 1 1 1 1 1 RL 1 1 1 LR 1 4 1 1 RL 1 1 1 LR 1 1 2 RL 0 LR 1 RL 0 L
VWI R 5 2 3 1 RL 1 1 1 1 1 1 LR 2 4 2 RL 1 1 3 1 1 1 1 1 1 LR 3 2 8 1 4 1 RL 1 3 1 LR 1 1 4 1 # 1 1 RL 1 8 L
BWS R 7 6 6 2 7 1 5 5 1 3 1 RL 0 LR 6 7 7 2 6 1 5 4 1 3 1 RL 0 LR 6 7 7 2 6 1 5 3 1 3 1 RL 0 LR 2 2 2 2 2 1 2 2 1 2 1 RL 0 L
BWE R 1 7 6 6 2 8 1 6 6 1 4 2 RL 1 1 1 1 1 1 1 1 1 1 1 LR 1 5 5 5 2 6 1 6 5 1 4 2 RL 1 LR 1 1 5 4 3 2 6 1 5 8 1 5 2 RL 1 1 1 1 1 1 1 1 1 1 1 LR 1 1 3 3 3 2 4 1 4 5 1 6 2 RL 1 1 1 1 1 2 1 2 2 1 2 2 L
BWG R 9 5 RL 5 5 LR 3 2 RL 2 2 LR 0 RL 0 LR 4 2 RL 2 2 L
HR R 0 RL 0 LR 5 1 RL 1 1 LR 0 RL 0 LR 4 1 RL 1 1 L
SBP R 1 3 1 2 1 1 1 1 RL 1 1 1 1 1 1 LR 1 2 1 7 2 2 1 1 RL 1 2 2 1 1 LR 1 1 1 2 1 3 2 RL 1 1 1 1 2 2 LR 1 1 1 4 1 RL 1 1 L
C
A
I1
I10
C
A
I1
I10
C
A
I1
I10
C AC A I1 I10 I1 I10C A I1 I10C A I1 I10C A I1 I10C A I1 I10C A I1 I10
C
A
I1
I10
C
A
I1
I10
C
A
I1
I10
C
A
I1
I10