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Flashcards in GiM Lecture 1,2,3 Deck (50):
1

Reasons for clinical genetics referrals

Child
Birth anomalies, dysmorphic features, learning difficulties

Adult
Diagnosis, predictive testing, carrier testing, family history, foetal loss/recurrent miscarriage

Pregnancy
genetic disorder, screening abnormality

2

What is genetic counselling

Education process to assist affected or at risk individuals understand the nature of genetic disorder, transmissions and available options

3

How are genetic diagnosis made

Family tree - pattern of inheritance
Physical examination
Genetic Tests - Chromosome, Genes

4

Testing For genetic disorders
- Non genetic tests
- Genetic tests

Blood tests
-Enzyme assays
-Inborn errors of metabolism

Haematology
-thalassaemia
X Rays
-Skeletal dysplasia

Genetic
Genomic architecture
-Cytogenetics
-Array based techniques
Gene faults
-Sequencing
-OLA assays
-MLPA tests

5

Advantages and disadvantages of genetic testings for disorders

Advantages
-Early diagnosis
-Early interventions
-Carrier testing
-Reproductive choices
-Prenatal testing

Disadvantages
- no treatment
- does knowing help

6

What is Pharmacogenomics

Analysis of entire genomes of a group
aim to identify genetic factors influencing response to a drug

7

What is pharmacogenetics

Study an individuals genetic make up to predict drug response and guide prescription

8

What is Glevec

Treatment for CML (chronic myeloid leukemia)
Targeted at novel fusion protein which is the product of translocation in CML

9

What are contributions to human diseases

genetic
environmental

10

Define
- Multifactorial genetic disorder

the interaction of multiple genes (genetic predisposition) in combination with environmental factors eg type II diabetes, ischemic heart disease.

11

define
- single gene genetic disorder

a mutation in a single gene = Mendelian inheritance – AD, AR, XL eg cystic fibrosis

12

Define -
Chromosomal genetic disorder

an imbalance or rearrangement in chromosome structure eg aneuploidy, deletion, translocation

13

Define
- Mitochondrial genetic disorder

a mutation in mitochondrial DNA

14

Define
- somatic mutations

mutation(s) within a gene(s) in a defined population of cells that results in disease eg breast cancer

15

What are the single gene modes of inheritance

Autosomal Dominant
Autosomal Recessive
X-linked
Mitochondrial

16

What is Autosomal dominant inheritance

- What does it mainly affect
- give 3 examples of autosomal dominant conditions

A trait or disease runs from one generation to the next

Males and females equally affected

Offspring of affected person has a 50% (1 in 2) chance of inheriting the mutation

Structural proteins, receptors, transcription factors

Myotonic dystropy
Marfan Syndrome
Huntingdon Disease

17

Autosomal Dominant Inheritance
- What genotype are those affected
- What is the change off spring is
a) affected
b) unaffected

Affected = 50%
Affected = heterozygous

Unaffected - 50%
Homozygous

18

What is Penetrance?
- give example of a disease with 100% penetrance

The frequency with which a specific genotype is expressed by those individuals that possess it,
e.g huntingdons has 100% penetrance

19

What is expressivity

variation in expression - the extent to which a heritable trait is manifested by an individual

e.g. marfan - aortic dilation --> stretch marks

20

What is anticipation?
- two disease examples

the symptoms of a genetic disorder become apparent at an earlier age as it is passed from one generation to the next. In most cases there is an increase in the severity of symptoms too
- myotonic dystrophy
- huntington's disease

21

Define
De Novo Mutation

new mutation that has occurred during gametogenesis or in early embryonic development.

22

Explain Autosomal Recessive inheritance

- give examples of autosomal recessive inheritance diseases

-Disease seen in one generation
-consanguineous relationship increases risk of disease offspring
-relatives maybe carriers
-affects M and F equally
-Gene mutations not chromosomes

- cystic fibrosis
- metabolic disorders
- haemachromatosis
- sickle cell

23

Autosomal Recessive inheritance
- What genotype are affected
- What risk of being affected
- risk of being an unaffected carrier

Affected = homozygous or compound heterozgous
Affected = 25%
unaffected Carrier = 2/3
unaffected = 25%

24

X linked inheritance
- Explain
- Example diseases

Males affected
Females - spectrum - unaffected --> fully
M usually more affected
Female transmission ONLY
Possible in
- Gene mutations, chromosome deletions and duplications

Duchenne Muscular Dystrophy
Fragile X syndrome
Red/green colour blindness
Haemophilia

25

X linked inheritance - Carrier Mother
- Affected Boy
- Carrier Girl
- Normal Boy
- Normal Girl

25%

26

X linked inheritance - affected father
- daughters?
- Sons?

D = All carriers
S = unaffected - no male transmission

27

X linked inheritance
Why can females have varying phenotypes

X inactivation
XL dominant vs XL recessive inheritance

CANNOT predict female phenotype in prenatal testing

28

What is Lyonisation?

-X- inactivation
-One X chromosome in cells with XX is turned off.
-Occurs in early embryogenesis
-Most but not all inactivated X genes turned off.

29

X inactivation and disease expression
What is skewed X inactivation?
What is tissue variability

Skewed = random preference for normal X chromosome to be inactivated over abnormal X

Tissue - Random prefernece for mutated X chromosome to be active in crucial tissue group

30

X linked Dominant inheritance
- Affects?
- Who does Rett syndrome effect
- Who does Fragile X syndrome effect

Males and females
Rett - lethal in M, phenotype only in F

Fragile X - M affected, F - spectrum

31

X linked Recessive
- affects?
- are carrier girls affected?

Affects - males,
carrier females
can be affected F is homozygous

carrier girls - affected if x inactivation skews

32

Mitochondrial Inheritance
- explain
-example

- Maternally inherited diabetes and deafness

- Rare , M = F affected
- only 27 genes in mitchondrial DNA
- always maternally inherited
- affected mother = ALL offspring affected
- affected father - no affect

33

Family trees
What does .... mean?
- Circle
- square
- diamond
- diamond crossed out
- triangle
- triangle crossed out
- filled circle/square
- square/circle with dot

- female unaffected
- male unaffected
- unknown sex
- still born unknown sex
- miscarriage
- abortion
- affected F/M
- asymptomatic carrier

34

What is the symbol for
- Consanguinity
How does it affect genetics

Double line between couple
- blood relative
- congenital birth defect 5-6% risk (pop normal = 2-3%)

35

What is Polymerase chain reaction

In Vitro synthesis of large amounts of DNA

Oligonucleotides define boundaries of synthesis

DNA synthesized by DNA polymerase enzyme

1) Heat denaturation 94 degree
2) primer annealing 55 degree
3) primer extension 72 degree

Products separated by GEL electrophoresis and visualized with UV

36

What can be determined by PCR

Presence/absence of something
- allele specific PCR

product size by gel electrophoresis
- Oligonucleotide ligation assay
- direct sequencing

37

How does gel electrophoresis work

Electrical current
small products move towards +ve end
large products remain at -ve end

DNA is -ve charged therefore moves towards +ve

38

What is the mutation for the most common inherited cause of deafness

Connexin 26
(GJB2)

39

What can a delta35g assay show

accurate size analysis - can show single base deletions
- able to distinguish
hetero zygotes, homo zygotes, and normal

40

What is Allele specific mutation
detection
- method
- use

- distinguish between 2 alleles that differ by one nucleotide
aka - Oligonucleotide Ligation Assay

- allele specific primer- 3' nucleotide base pair with changed nucleotide
- reaction will not occur if base pair not perfect
- able to tell abnormal from normal alleles

41

How can Cystic fibrosis gene mutations be identified

Cystic Fibrosis genotyping assay

42

What is Multiplex Ligation- dependent probe amplication analysis (MLPA)

- detects chromosomal DNA copy number changes in multiple targets

43

What is the amount of product from PCR proportional to?

the amount of target DNA present

44

What are the problems with mutation anaylsis

gene might be too big for PCR
gene may be repetitive
GC rich regions are hard to PCR

45

Souther Blotting is used for what?

Fragile X syndrome
DNA

46

what is DNA sequencing

Detection of unknown mutations
= exact position of mutation
- type of mutation
uses specific PCR product as template

47

What nucleotides are used in sequencing?

dNTP deoxyribose nucleotides
dideoxyNTP dideoxyribosenucleotides

48

how do ddTTPs help with sequencing

stop chains continuing to grow
lots of chains different lengths
can read sequence by gel electrophoresis

49

What is MEGF10 mutation screening

distinguish between different muscular dystrophies

50

What is clonal sequencing

next generation
Illumina Method
Long PCR product covering gene
produces flow cell images