zurich molecdiagnostics2017 final

Molecular Diagnos/cs 2017 – [email protected]

Common and rare variants influencing blood pressure

Georg Ehret, MD CC FAHA

Cardiology, University of Geneva & Geneva University Hospital


Use of gene/c data to inform cardiovascular care, the example of blood pressure

JAMA 2016


Large genomics studies : examples

Budget: 215mio USD

www.whitehouse.gov/precision-‐medicine www.dor.kaiser.org/external/DORExternal

KAISER insurance Example of EHR-‐based study

500’000 parTcipants

Rare disease

TradiTonal populaTon-‐based and clinical studies. Sample sizes in general <20k parTcipants.


Blood pressure genomics as an example cardiovascular complex phenotype

Types of BP genetics.

Results from genome-wide association studies (GWAS) and how we can learn from them.

A self-experiment using 23andMe.


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Prevalence of HTN in Switzerland

Danon-‐Hersch et al. European journal of Cardiovascular PrevenTon and RehabilitaTon 2009;16:66; Guesous PLoS ONE 7(6): e39877; 2012.

•  CoLaus Study: 6,182 parTcipants from 2003-‐2006 •  35-‐75y •  52% female

•  HTN in 36%

•  SWISSHYPE (2009 survey on 1,376 hypertensives) •  65+-‐12y •  54% male


Stroke mortality by 14%

CHD mortality by 9%

All-‐cause mortality by 7%

SBP by 5 mmHg:

Popula/on effect of BP reduc/on

Analysis of 5 major observaTonal studies:

Lewington et al. Lancet 2002; 360:1903


environment gene/cs

Causes for the distribu/on of quan/ta/ve traits

X ~ Ν(μ,σ2)

1 Levy et al. Hypertension 2000;36(4):477-‐83. 2 Poulsen et al. Diabetologia 1999;42(2):139. 3 Pilia et al. PLoS Genet 2006;2(8):e132 4 Nora et al. CirculaTon 1980;61(3):503-‐8. Kurt Stern, Benefon, controllinghighbp.com


• SNPs –  most frequent type of variaTon (38m SNPs in 1000G) –  variant load per individual: ~4m (1000G)

type

• others –  INDELS and CNV (1.4m INDELS in 1000G). –  EpigeneTc modificaTons.

SNP

INDEL

Human genome and gene/c varia/on

HapMap ConsorTum, Nature 2005;437:1299; 1000G consorTum, Nature 2012;491:56

Popula(on level: -‐  common SNPs: >5% MAF -‐  low frequency SNPs: 0.5-‐5% MAF -‐  rare SNPs <0.5% MAF


The older a variant, the more frequent it generally is.

-‐> Common trait – common variant hypothesis.

Popula/on history and frequency of variants

Aravinda ChakravarT, Nature GeneTcs 1999;21:56


Manolio et al, Nature 2009; 461, 747-753

Allele frequency and effect size


Blood pressure (BP): monogenic and quan/ta/ve trait

Classic gene/c quan/ta/ve trait

Victor McKusick, CirculaTon 1960;5:857; Mayan H et al. JCEM 2009;94:3010-‐3016

Families with “Licon genes” ( e.g. familial hyperkalemic hypertension)


Monogenic hypertensive syndromes: “Licon genes”

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!Ehret et Caulfield, EHJ 2013 Apr;34(13):951-61


BP in the general popula/on

•  No significant contribuTon by the monogenic BP variants (they are all very rare).

•  No significant contribuTon by the genes in known BP pathways (these have been sequenced in large numbers).

Molecular Diagnos/cs 2017 – [email protected] source: NHGRI 2012, http://www.genome.gov/sequencingcosts; BBC; Nanopoore, Affymetrix, Illumina

Technological development of large-‐scale genotyping in 2000-‐2005

La technologie « microarray » permet de génotyper des millions de SNPs en une expérience.

Le génotypage / séquencage devient plus accessible.

Le coût pour le génotypage / séquencage baisse plus rapidement que la loi de Moore.

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2002 2004 2006 2008 2010 2012

temps

10k$

100k$

1mio$

10mio$

100mio$ ● coût par génome

interroga/on non-‐biasée d’un grand nombre de variantes dans tout le génome

= génomique


Complex trait genomics 2005-‐2016

GWAS findings: end 2005 End 2016


Genome-‐wide associa/on studies, cont. Associa/on

genotype XY: 5 (of 6) 1 (of 6)

χ2 = 5.3 p = 0.03

No. of markers usually u/lized: ~>106

1Chakravarti, Nature Genet. 19, 216–217 (1998)

SNP


Genome-‐wide associa/on studies: Mul/ple tes/ng adjustment

No. of markers usually ~>106

Significance threshold: P = 0.05/1,000,000 P = 0.00000005 = 5x10-8

(Bonferroni)


State of HTN/BP GWAS in 2007 WTCCC GWAS 2007: cardiovascular traits or risk factors: 2,000 cases / 3,000 ctr.

WTCCC, Nature. 2007 Jun 7;447(7145):661-‐78.


Power of BP GWA studies

EHJ 2013 Apr;34(13):951-61

The effect size observed for BP per variant is ~1mmHg = ~0.05 SD for SBP


1) The GWAS BP loci are largely in regions previously unknown to be relevant for BP

Five observa/ons from BP genomics studies.

Example from 2009 GWAS: Gene name(s) near each locus

Ehret et al. Nature. 2011 Sep 11;478(7367):103-9


2) The number of associated variants is large and their frequency is generally common (average MAF ~30%), there are only few examples of uncommon / rare variants.



Trait Typical absolute effect size of one SNP

Effect explained (of total phenotype varia/on)

SBP/DBP ~1/0.5 mmHg ~3-‐4% LDL/HDL/TG ~0.02mmol/L ~10% diabetes ~6%

3) Typical effect sizes per risk allele are small and liple of the total trait variance is explained.

Ehret et al. Nature. 2011 Sep 11;478(7367):103-‐9. Locke et al. Nature. 2015 Feb 12;518(7538):197-‐206 Willer et al. Nat Genet. 2013 Nov;45(11):1274-‐83.



AssociaTon with BP in non-‐white ethnici/es using a 29-‐SNP risk score:

*per SD of the 29-‐SNP risk score

Ehret et al. Nature. 2011 Sep 11;478(7367):103-9.

4) The same BP variants appear to act in all ethnici/es.



Santhi K. Ganesh

Aravinda ChakravarT

LTA in 48,564 European participants: up to 4 measurements averaged within a 15 year time-span, visits were at least one year apart.

SBP DBP

Correlation between LTA and “single visit” phenotype:

Five observa/ons from BP genomics studies. 5) Improved phenotype precision seems to help iden/fica/on of BP loci.


ICBP LTA analysis

p <5x10-‐7

SBP

DBP

p< 5x10-‐8

Across all phenotypes 20 loci reach genome-wide significance. Of these 4 are new (chr2:26Mb, chr2:96Mb, chr6:43Mb, chr7:45Mb) and replication was attempted in 40,254 individuals with single visit association results (GBPGen).

single visit

single visit

LTA

LTA


What is this informa/on useful for?

•  InvesTgaTon of cause-‐effect relaTonships. •  IdenTficaTon of new pathways. •  IdenTficaTon of causal Tssues.


Mendelian randomiza/on studies


Mendelian randomiza/on of BP effects using 66 SNPs

Ehret, Fereira et al, Nature GeneTcs 2016


Ehret et al., Nature Genetics 2016 Hoffmann, Ehret et al., Nature Genetics 2016

1)  Using DNase hypersensitivity sites of 123 cell types: enrichment of marks at BP-associated SNPs in microvascular endothelial cells

2)  Expression data from GTEx:

enrichment in arterial tissues.

Enrichment and pathway analyses


Summary epidemiology and gene/cs of BP

•  HTN is quan/ta/vely the most important cardiovascular risk factor and HTN is sTll poorly controlled.

•  The geneTc underpinnings of primary hypertension are hundreds to thousands of SNPs with small individual effect sizes.

•  The kidney might not be a major causal organ for primary hypertension, is it the vascular endothelium?

•  Currently genomics *cannot* guide treatment for primary hypertension.


“direct to consumer” DNA tes/ng

Others: Navigenics, deCODEme, …


23andMe

www.23andme.com

•  Mission: “23andMe's mission is to be the world's trusted source of personal gene/c informa/on” •  About 200’000 SNPs are genotyped •  Cost ~100CHF


23andMe: Company des/ny

www.23andme.com

The FDA has now severly reduced the amount of diagnosTc informaTon that 23andMe can provide.


Overall summary

•  Complex geneTc traits are generally not ready for diagnos/c laboratory tes/ng.

•  There are appealing and interes/ng other avenues how to use geneTc informaTon on complex traits for our paTents.


Acknowledgments Consor/a and studies InternaTonal ConsorTum for Blood Pressure Genome-‐Wide AssociaTon Studies (ICBP)

CardioMetabochip – ICBP consorTum

Cohorts for Heart and Aging Research in Genome Epidemiology (CHARGE) – BP consorTum

Atherosclerosis Risk in CommuniTes Study (ARIC) (PI for BP genomics: Aravinda ChakravarT)

SKIPOGH study (PI: Prof. Murielle Bochud)

Prof. Aravinda ChakravarT and Prof. François Mach

Personal grant support Swiss NaTonal FoundaTon Geneva University Hospitals FondaTon pour Recherches Médicales NHLBI

zurich molecdiagnostics2017 final

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