genetic association and gene mapping

Question 1

health and disease

Answer 1

relationship between genetics and environment- GxE interaction resulting in certain health outcome
understanding of how the environment effects is poor due to many factors that can affect an individual, health outcomes change between individuals
epigenetics- change the gene expression but dont alter the gene itself

Question 2

complex disease/ phenotype

Answer 2

common- high incidence - large no. of people affected
non mendelien transmission- parents may not have the disease but child may be a sufferer
clustering in families- may be more likely in familes due to sharing the environment
complex aetiology- how the disease is caused
oligogenic- a few genes
polygenic- many genes

Question 3

polygenic inheritence

Answer 3

additive- sum of effects of 2 or more gene loci
multiplicative- combines effect of 2 or more gene loci
epistasis- gene-gene interactions, suppressive or stimulatory

Question 4

gene mapping methods

Answer 4

two main statistical methods
- linkage analysis- based on recombination frequency
- follows meiotic events through families for co-segregation of disease and particular genetic variants

• association analysis- based on LD

Question 5

linkage

Answer 5

family based
matching/ethnicity is generally unimportant
few markers for genome coverage
good for initial detection but poor for fine mapping
powerful for rare variants
can be weak design- low resolution

Question 6

association

Answer 6

unrelated individuals
matching/ethnicity is crucial
many markers require for genome coverage
poor for intiial detection, good for fine mapping
powerful for common variants- rare variants generally impossible
powerful design - high resolution

Question 7

genetic association

Answer 7

test for correlation between disease status and genetic variation
SNPs are most widely used markers- microsatellites markers, insertion/deletion, VNTRs, CNVs also used
is major tool for identifying genes conferring suscebtinility to complex disorders

Question 8

genetic association analysis

Answer 8

analytic method to confirm presence of genetic factors in diseases at population level
two approaches
- candidate gene analysis
- genome wide scan

Question 9

candidate gene analysis

Answer 9

hypothesis driven studies, cheaper and easier to carry out
dont need larger no. of individuals and genetic markers
screen genes for mutations that may affect function

Question 10

genome wide association scan (GWAS)

Answer 10

hypothesis free, scan entire genome using highly polymorphic dna markers, directly screen known genes in linked regions for mutations, looking at many patients and controls

Question 11

association analysis + LD

Answer 11

LD is the non random association of alleles at different loci
human genome- look for an association between an allele frequency and its LD with other genetic markers surrounding it
LD makes tightly linekd variants strongly correlated, producing cost savings for association studies- possibility of identifying association with the disease by direct susceptibility marker (direct association) or a marker that is in high LD with susceptibility marker (indirect association)

LD is affected by mutation, recombination, genetic drift and natural selection

Question 12

LD explained

Answer 12

LD (allelic association) - particular alleles at two or more neighboring loci show allelic association if they occur together with frequencies significantly different from those predicted from the individual allele frequencies

non random association of alleles at 2 or more loci

Question 13

case contorl

Answer 13

approach common in association studies
controls have to be from same population
aim to detect association between one or more genetic markers

adv
- methodology is well known
- convenient to collect large samples
- more efficient recruitment than family based sampling

dis
- population stratificaion
- need for highly dense marker sets
- lack of phase info
- inconsistent results

Question 14

odds ratio

Answer 14

tells us what the effect the genetic marker has on the disease
1= genetic marker is not contributing - not increasing or decreasing risk
>1= marker is increasing the risk (positively associated to disease)
<1= marker is decreasing the risk- protecting against disease (negatively associated to the disease)

calculated in 2x2 tables
- is not a proportion but the ratio of the number of ways an event can occur relative to the number of ways it cant occur

Question 15

original basics methods (woolfs)

Answer 15

most common and simple
can be used with any marker- genotype, allele etc
robust, allows combining of data requires patients and controls

table
a- patients with a marker
b- controls with marker
c-patients without marker
d- controls without marker

Question 16

steps in association analysis

Answer 16

work out odds ratio
work out significance of association- use row x column chi sqaure
work out expected numbers
usuing x2 can assess observed value against critical value
x2>CV indicates significant association

Question 17

confidence interval calc

Answer 17

CI for odds ratio is calculated on the natural log (Ln scale) then converted back to original scale
point estimate ± confidence coefficient x SE
PE=odds ratio natural log
CC= 1.96
sampling distribution of OR is positively skewed, approx normally distributed on Ln
OR above 1, X2 significant CI not passing through 1 or above 1= significant susceptibility
OR below 1, X2 significant , CI not passing through 1= significant protection
OR below =1, no sig x2 and CI passing through 1- no effect

Question 18

association analysis steps

Answer 18

1. create 2x2 table
2. work out odds ratio
3. check statistical significance using x2
4. work out CI of odds ratio
5. interpret date

Question 19

problems with genetic association studies

Answer 19

population stratification- differences between cases and controls
genetic heterogneity- different genetic mechanisms in different populations
random error- false positives/negatives
study design/ analysis problems- poorly defined phenotypes, poor control group selection + small sample sizes, replication failure

Question 20

genetics of complex disease

Answer 20

multiple genes and multiple factors that can affect the disease
many environmental factors can also affect

Question 21

diabetes

Answer 21

complex aetiology- multiple phenotypes
due to insulin resistance or insulin deficieincy
life-long controllable condition
type 1- no insulin produced
type 2- body does not use insulin properly (resistant)

Question 22

diabetes risk factors

Answer 22

age
stress
family history
poor diet
increased weight
genetics
smoking

Question 23

diagnosis

Answer 23

oral glucose tolerance test
fasting plasma glucose
A1C

Question 24

type 1

Answer 24

autoimmune disease results in the bodys failure to produce insulin
only 5-10%
frequent urination, unusual thirst, extreme hunger

Question 25

tyep 2

Answer 25

results from insulin resistance and relative insulin deficiency
more common and mostly seen in adults
blurred vision, usually obese

Question 26

gestational

Answer 26

high blood sugar (glucose) levels during pregnancy

Question 27

genetics of type 1

Answer 27

main candidate gene- HLA (chromosome 6) and insulin
HLA- DR gene , DR3 and DR4 allele susceptible
DR3- develop diabetes later
DR4- develop diabetes earlier
those who inherit both develop young age diabetes
DR2 protects against tyepe 1

insulin gene (c11)
codes for insulin and determines amount of insulin made
many mutations and polymorphisms

Question 28

type 2 genetics

Answer 28

group of genetically heterogenerous metabolic disorders that cause glucose intolerance
~90% of individuals with diabetes have T2D
polygenic and multifactoral- causes by multiple factors that may interact- environment and risk fctors
different symptims develop over time

Question 29

insulin resistance

Answer 29

glucose cant enter cells efficiently so too much circulates in bloodstream
glucose enters blood stream, insulin enters blood stream
cell doesnt respond to insulin so cell cant open for glucose to enter
glucose cant enter cells so too much of it circulates in bloodstream

hyperglycemia- high blood sugar

Question 30

environmental risk factors of T2D

Answer 30

increased risk of developing T2D when BMI>30
~80% of newly diagnosed cases due to obesity
higher association with abdominal or central obesity
physical inactivity increases risk

Question 31

type 2 genetics- how mamy genes

Answer 31

monogenic (~2%)- maturity onset diabetes of the young
syndromic (~1%)- maternally inherited diabetes and deafness, severe insulin resistance
overlap (~5%)- latent autoimmune diabetes of the adult
polygenic (~90%) candidate genes and GWAS
individuals with family histiry 2-6 x more likely to develop
higher concodrnace for MZ V DZ twins

Question 32

finding genes for T2D

Answer 32

candidate genes selected as they are involved in pancreatic beta cell function, insulin action, energy intake and lipid metabolism
GWAS- current approach based on 1000s of cases and controls- millions of SNPs

Question 33

CAPN10

Answer 33

chromosome 2q37.3
encodes intracellular dependent cytoplasmic protease that is ubiquitosly expressed
likely involved insulin secretion and resistance
stronger influence in mexican americans
2x increased risk

Question 34

Ppary

Answer 34

peroxisome proliferator activated receptor y
transcription factors play important role in adipocyte differentiaition and function
associated with decreased insulin sensitivity
target for hypoglyceamic drugs
increased risk 1-3x

Question 35

TCF7L2

Answer 35

related to impaired release of glucagon like peptide 1, reduced B cell mass and B cell dysfunction
estimated relative risk 1-4x

Question 36

GWAS

Answer 36

goal to find connections between phenotype and whole genome genotype
whole genome genotyping- affymtrix and illumine
GWAS promise we will identify genetic basis for this heritability
have found a few of the strongest associations are in coding regions, most associations in regulatory elements

Question 37

missing heritability

Answer 37

where is the missing heritability
1. rare variants not covered by GWAS- every family has own mutations, rare mutation analysis requires whole genome sequencing
2. complex associations/epistasis-combinations of SNPs
3. lack of power/effects are weak so need much more data
4. epigenetic effects- heritability may not be in the genome at all

Question 38

thrifty genotype

Answer 38

had a selective genotype
in past, individuals who were metabolically thrifty were able to store a high proportion of energy as fat so more likely to survive famine
recently, populations have continuous supply of calorie dense processed foods + reduced physical activity
changes may explain rise in T2D but consistent evidence is missing

Question 39

prevention of T2D

Answer 39

maintaining age appropriate body weight
balanced diet and phsyical activity