Genome wide scan studies and Strategies of defining QTLs

1. Taher Bohari
Roll no-09
2nd Semester
M.S (Pharm)
Pharmacology & Toxicology
1

2. • Introduction
• Ideal properties
• Models for Hypertension
• Genetic models
• Heterogeneity
• Genome wide scan
• Recent advance in genetics of HTN
• Single nucleotide polymorphism
• Strategies for defining QTLs
• Conclusion
• Reference
2

3. Hypertension – Blood pressure > 140/90 mm Hg
Classification of blood pressure according to JNC 7
Blood pressure
classification
SBP (mm
Hg)
DBP (mm
Hg)
Normal <120 And < 80
Pre hypertension 120-139 Or 80-89
Stage 1 Hypertension 140-159 Or 90-99
Stage 2 Hypertension >160 Or >100
Garg et al. (2017) 3

4. • It should be feasible in small animals.
• It should be simple to perform and uniformly reproducible.
• It should be able to predict the potential antihypertensive
properties of an agent.
• It should consume minimal quantities of compounds.
• It should be comparable to some form of human
hypertension.
Badyal et al. 4

5. 0
500
1000
1500
2000
2500
3000
Fig 1-Absolute number of papers
published on hypertension in
different species, rat, mouse, dog
and cat. It is evident that
hypertensive rats are the most
often used species in hypertension
research.
0
2
4
6
8
10
12
Fig 2-Number of publications on a
particular rat model of hypertension,
as divided by the total number of
papers on hypertension.
Numberofpublications(%ofpublicationsonHTN)
Pinto et al. (1998) 5

6. Hypertension
Etiology
Secondary
renal
2K1C
endocrine
DOCA-salt
Primary
genetic
SHR, Dahl etc.
environmental
Stress model
Pinto et al. (1998) 6

7. The recent advances in molecular genetics and genomics have provided
powerful tools to study the genetics of multifactorial diseases, such as
hypertension.
With the advent of “comparative genomics,” the application of genetic
studies to both human and animal model systems allows for a new
paradigm, where comparative genomics can be used to bridge between
model utility and clinical relevance.
Stoll et al. (2001) 7

8. Spontaneous Hypertensive Rats (SHR)
 Developed in 1963 by Okamoto and Aoki
 Required no physiological, pharmacological or surgical
intervention
 In SHRs, BP gradually increase until it is maintained markedly
elevated
level after approx. 12 week of age
 SHRs develop not only moderate to severe hypertension but also
typical
complications of hypertension.
 The SHR stroke prone (SHR-SP) is a further developed sub-
strain, with
even higher levels of blood pressure, and a strong tendency to
die fromPinto et al. (1998) 8

9. Dahl salt-sensitive rats
 This rat was bred in the 1950s
 The salt sensitive Dahl rats develop severe and fatal hypertension
when fed
high salt diets, whereas salt resistance rats do not develop such
hypertension
upon salt loading
 The salt sensitive rats become hypertensive, demonstrating that this is
a model
of genetic hypertension, with extra feature of salt sensitivity
Pinto et al. (1998) 9

10. Rat chr 1, 2, 10, and 13
BP QTLs confirmed
Yielding QTL on rat chr
Genome wide scan using
different genetically
hypertensive rat strains
Fig – Genome wide scan in genetically hypertensive rat
strains
Stoll et al. (2001)
Genome wide scan
10

11. Blood pressure is a difficult phenotype due to the complexity of its
physiologic regulation and the multiplicity of pathways, and hence the
likelihood of a large number of genes involved.
While some investigators believe positional cloning of QTLs to be too
hard , but this problem can be overcome with the improving
infrastructure in genomic research.
The genetic basis of hypertension is best understood in monogenic
forms of hypertension associated with syndromes such as Liddle’s
syndrome with the identification of causative mutations in a single gene
locus
This syndrome is caused by
irregulation of the
epithelial sodium
channel (ENaC) due to a
genetic mutation at the 16p13-
p12 locus
Stoll et al. (2001)
Recent advance in genetics of HTN
11

12. SNPs are common bi-allelic markers that occur approximately every
500 to 1000 base pairs in the human genome
SNPs have the potential as powerful tools for the detection of
functional polymorphic variants that are involved in the genetics of
complex diseases especially if these SNPs are part of coding
sequence.
Single-nucleotide polymorphism
Stoll et al. (2001) 12

13. Using comparative maps for rat and human genomes, a strategy is
developed for translating QTLs across species, with emphasis on
using the linkage data obtained from rat studies for prediction of
susceptibility regions for hypertension in humans.
Stoll et al. (2001) 13

14. BP QTLs in
human genome
Study BP QTLs in rat
genome
Study
1q23–1q32 Mansfield et al. Chr 2, Chr 13 Stoll et al., Dubay
et al, Kato et al.,
Kurtz et al.,
Pravenec et al
2q23.2 Krushkal et al. Chr 3 Stoll et al.
5q31.1–5qter Krushkal et al. Chr 18, Chr 10 Jacob et al., Stoll
et al.
7q21–22 Xu et al Chr 12 Kato et al.
8q22 Curnow et al. Chr 7 Garrett et al,
Cicila et al.
1p Rice et al. Chr 2 Stoll et al., Schork
et al.
14

15. BP QTLs in
human genome
Study BP QTLs in rat
genome
Study
2p13–2p16 Krushkal et al. Chr 3, Chr 4 Stoll et al.,
Schork et al.
7q Rice et al. Chr 4 Stoll et al.,
Schork et al.
15q25.1–15q26.1 Krushkal et al. Chr 8 Stoll et al.,
Schork et al
17q Julier et al.,
Baima et al.,
Mansfield et al.,
Levy et al.
Chr 10
Chr 5
Chr 9
Jacob et al.
Stoll et al.
Rapp et al
Stoll et al. (2011) 15

16. Overall mean of
150 mmHg
Example
BP QTL
A, B, C, D and E
loci of 5 diff chr for
BP
A1,B1, C1, D1, and E1.
Minus allele
8 × -5 = -40
mmHg
A2, B2, C2, D2, and E2
Plus allele
2× +5 = +10
mmHg
Plus and minus effect is
-40 + 10 = -30 mmHg
Over all mean
150 yields 120 in
1st individual
Strategies for defining quantitative trait
loci for blood pressure
16

17. The BP for the other individuals are calculated
similarly
Individual Genotype Blood pressure
1 A1A1B1B2C1C1D1D2E1
E1
120 mmHg
2 A2A2B1B1C1C1D1D1E1
E1
120 mmHg
3 A1A2B2B2C1C2D1D1E1
E2
150 mmHg
4 A1A1B2B2C2C2D2D2E2
E2
180 mmHg
Rapp et al. (2000) 17

18. The identification of susceptibility genes for multifactorial diseases
such as hypertension remains challenging and will most likely require
the combination of multiple approaches to prove the causality of a
given susceptibility factor in the pathogenesis of the disease.
Considering the wealth of physiologic, pharmacologic, and genetic
information that has been collected in the rat in the past, the rat
represents an ideal model for functional studies
Conclusion
Stoll et al. (2011) 18

19. 1. Garg.G, Gupta.S, (2017). Review of Pharmacology, New Delhi,
Jaypee brothers medical publishers, 111-116
2. Stoll.M, Jacob.J, (2001). Genetic Rat Models of Hypertension:
Relationship to Human Hypertension, 3, 157-164
3. Badyal.D.K, Lata.H, Dadhich.A.P, (2003). Animal Models of
Hypertension and Effect of Drugs, 35, 349-362
4. Rapp.P, (2000). Genetic Analysis of Inherited Hypertension in the Rat,
80, 135-172
5. Pinto.M, Paul.M, Ganten.D, (1998). Lessons from rat models of
hypertension: from Goldblatt to genetic engineering, 35, 77-88
19

20. 20