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Phase 3 > Week 1 > Flashcards

Week 1 Flashcards

1
Q

What is the structure of DNA?

A

double helix strand

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2
Q

WHat are the 4 DNA nucleotide?

A

AGCT

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3
Q

What are the 4 RNA nucleotides?

A

AGCU

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4
Q

Which nucleotide does A bind to?

A

T

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5
Q

Which nucleotide does C bind to?

A

G

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6
Q

What nucleotide does T bind to?

A

A

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7
Q

What nucleotide does G bind to?

A

C

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8
Q

Between which nucleotides do stronger bonds form and why?

A

C-G because there are 3 hydrogen bonds instead of 2

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9
Q

Describe the process of gene expression

A 
RNA polymerase forms primary mRNA
mRNA undergoes splicing to remove introns and mature mRNA is formed
Translation then occurs in the ribosome.
Transfer RNA is involved in translation
1st amino acid is methionine.
Codon (mRNA)
anti-codon(tRNA)
Then post translational modifications occur
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10
Q

What relation is the child of your cousin?

A

First cousin once removed

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11
Q

What is meant by penetrance?

A

Chance that inherited mutation will lead to disease

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12
Q

How do you calculate the chance of someone developing a genetic form of cancer?

A

chance of inheriting mutation multiplied by the chance that the mutation will lead to disease

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13
Q

What capabilities must be acquired for a cell develop into cancer?

A

proliferative signalling
avoidance of apoptosis
bypassing replicative senescence
insensitivity to anti-growth signalling

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14
Q

WHat part of chromosomes are involved in replicative senescence?

A

telomeres

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15
Q

Describe tumour suppressor genes

A

normally inhibit progression through the cell cycle

Promote apoptosis or act as stability genes

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16
Q

Give examples of tumour suppressor genes

A

Rb
TP53
DNA repair (BRCA)

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17
Q

Describe proto-oncogenes

A

normally stimulate cell cycle

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18
Q

Describe how oncogenes are formed

A

1 copy of mutated proto-oncogene leads to gain of function effects

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19
Q

What is meant by wt?

A

wild type - normal (non-mutated copy of allele)

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20
Q

Describe stability genes

A

a type of TSGs
act to minimise genetic alterations
account for commonest hereditary cancer predisposition syndromes

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21
Q

Describe sporadic cancer

A

common
late onset
single primary tumour

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22
Q

Describe familial cancer

A

uncommon
early onset
often multiple primaries

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23
Q

How are most common familial cancers inherited?

A

autosomal dominant

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24
Q

How do you identify the risk of a cancer being hereditary?

A

more than one individual in the same family
affected by similar cancers or cancers at related sites with early onset
multiple primary tumours
early age of onset

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25
Q

WHat would a cancer family history clinic offer?

A

draw family tree and verify diagnoses
estimate likelihood of predisposing gene mutation
discuss screening, risk factors, preventative measures

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26
Q

What are the main mutations involved in hereditary breast cancers?

A

BRCA 1
BRCA 2
TP53
PALB2

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27
Q

Which BRCA mutation is more likely when there is a family history of ovarian cancer?

A

1

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28
Q

Which BRCA mutation is most likely when there is a history of male breast cancer?

A

2

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29
Q

WHat is meant by modifier genes?

A

loci that confer to increased susceptibility to cancer
these are common and each confers a small effect on increased risk
These are mutations outwith genes - enhancer and silencer parts that control the expression of neighbouring genes

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30
Q

WHat is the function of the BRCA1 and BRCA 2 proteins?

A

DNA repair by homologous recombination of double-strand breaks

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31
Q

what treatment may BRCA 1 and BRCA 2 carriers offered?

A

examinations
screening
prophylactic bilateral mastectomies
prophylactic oophorectomies

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32
Q

Which mutated genes can lead to ovarian cancer?

A

BRCA 1
BRCA 2
HNPCC - MLH1 or MSH2

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33
Q

Describe how olaparib works

A

selective lethality

BRCA cell uses different type of DNA repair mechanism involving PARP - this is inhibited by drug and causes cell death

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34
Q

WHat is PARP?

A

poly ADP polymerase

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35
Q

what is the main form of familial colonic cancer?

A

hereditary non-polyposis colon cancer

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36
Q

What is a rare form of familial colonic cancer?

A

familial adenomatous polyposis

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37
Q

Describe HNPCC

A

usually only a few polyps
uterus, stomach, ovary
Due to inheritance in mutation in MMR systemic genes (repairs point mutations)

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38
Q

Which genes are associated with HNPCC?

A 
MLH1
MSH2
MSH6
PMS2
these genes encode proteins that act together in a complex to carry out miss-match repair
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39
Q

Which eye condition is associated with familial adenomatous polyposis?

A

congenital hypertrophy of the retinal pigment epithelium

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40
Q

What is unusual about MYH polyposis?

A

autosomal recessive inheritance
attenuated form of FAP
base excision repair (BER) gene DNA glycosylase

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41
Q

WHat cancers can be caused by Li fraumeni syndrome?

A 
breast
brain
sarcoma
leukaemia
adrenocortical carcinoma
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42
Q

What mutation is involved in Li fraumeni syndrome?

A

TP53

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43
Q

What is TP53 involved in?

A

control of cell cycle, apoptosis and replicative senescence

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44
Q

what is typically meant by a mendelian disorder?

A

single gene

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45
Q

How many genes are there?

A

20-25 thousand

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46
Q

What type of inheritance is achondroplasia?

A

autosomal dominant

47
Q

Describe autosomal dominant inheritance

A

effects every generation
vertical pattern of inheritace
only need 1 faulty gene
males and females effected

48
Q

What is meant by variable expression?

A

2 people in the same family with the same mutation can have different severities of it

49
Q

What is meant by incomplete penetrance?

A

inheriting the mutation does not necessarily meant you are affected by the condition

50
Q

What is gonadal mosaicism?

A

When some of the germ cells have undergone mutation and therefore there is a small chance of it being passed on to a child

51
Q

What gene can effect the severity or penetrance in people who carry the BRCA2 gene?

A

FGFR2

52
Q

Give examples of AD conditions

A

inherited breast or colon cancer
ADPKD
NF1

53
Q

What are the clues that a condition is autosomal recessive?

A

usually horizontal pattern of inheritance
both males and females effected
there may be consanguinity in the family

54
Q

What is meant by consanguinity?

A

parents may be related to each other. This increases the risk that both will carry the same mutation

55
Q

Give examples of AR conditions

A

cystic fibrosis
phenylketonuria
spinal muscular atrophy
congenital adrenal hyperplasia

56
Q

What are the features of recessive X-linked conditions?

A

Knight’s move pattern
No male to male transmission
only males afffected

57
Q

Why can there be some “manifesting carriers” in recessive X-linked conditions?

A

Skewed X inactivation
Normally 50% of each X chromosome turned off, but if this balance is skewed then it can lead to a faulty gene being more highly expressed

58
Q

Describe X-linked dominant inheritance

A

Pattern is like AD but with no male to male transmission

Females more likely to be affected than males

59
Q

Give examples of X-linked dominant conditions

A

Vitamin D resistant rickets
incontinentia pigmenti
Rett syndrome

60
Q

What is meant by genetic anticipation?

A

mutation gets bigger as more repeats are added

increasing severity of onset in successive generations

61
Q

Give examples of conditions that involve genetic anticipation

A

Huntington disease
Fragile X syndrome
myotonic dystrophy

62
Q

What is meant by pseudo-dominant inheritance?

A

If an AR condition but has a very high carrier frequency or consanguinity - it appears like AD

63
Q

Give an examples of a condition that can show pseudo dominant inheritance patterns

A

Gilbert syndrome

64
Q

What is unusual about mitochondrial DNA?

A 
much smaller genome
circular
much smaller than nuclear DNA
37 genes
no introns
65
Q

Describe mitochondrial inheritance

A

inherited only from the mother
all children inherit it from the mother but to a variable extent
there is a threshold of the number of mutations that are required for disease to occur
heteroplasty
syndromes often affect muscle, brain and eyes

66
Q

What is the presentation of Huntingtons disease?

A

onset between 30 and 50
progressive chorea (involuntary movement)
dementia and psychiatric symptoms

67
Q

What repeat is found in HD?

A

CAG

mainly prone to expansion during meiosis in the father

68
Q

Describe the pathophysiology of HD

A

CAG repeat within the coding sequence
encodes polyglutamine tract
expansion of tract causes insoluble protein aggregates and neurotoxicity

69
Q

Describe the clinical aspects of myotonic dystrophy

A

AD with genetic anticipation
progressive muscle weakness in early adulthood
also myotonia and cataracts
more risk of increased repeat sequence in mother

70
Q

Describe the genetic basis of myotonic dystrophy

A

unstable length mutation of a CTG repeat
in the 3’ transcribed but untranslated region of DMPK gene
affected if 50 or more repeats

71
Q

Describe the pathogenic mechanism in myotonic dystrophy

A

abnormal DMPK mRNA
indirect toxic effect upon splicing of other genes
e.g. the chloride ion channel gene (causing myotonia)

72
Q

Describe the clinical aspects of cystic fibrosis

A

AR
carrier frequency of 1 in 20-25
recurrent lung infections
exocrine pancreas insufficiency

73
Q

How is CF diagnosed?

A

screening of newborns by immunoreactive trypsin (IRT) level

confirmation by DNA testing and or sweat testing

74
Q

Describe the pathogenic mechanism of CF

A

CFTR mutations
defective chloride ion channel
increased thickness of secretions

75
Q

Describe the most common mutation in cystic fibrosis

A

F508del
in frame deletion of 3bp (one codon)
loss of phenylalanine (F) at position 508
prevents normal folding of protein and insertion into the plasma membrane

76
Q

What is meant by cascade screening?

A

identification of mutations permits prenatal diagnosis if desired and subsequent identification of carrier relatives

77
Q

Describe NF1

A 
neurofibromatosis 1
commonly cafe au lait macule and neurofibromas
short stature
macrocephaly
learning difficulties 
very variable expressivity
lisch nodules in eyes
78
Q

What are the possible complications of NF1?

A 
increased risk;
hypertension
scoliosis
pathological tibial fractures
significant tumours
79
Q

Describe the DMD gene

A

Largest human gene but doesn’t encode the largest protein

80
Q

What does dystrophin normally do?

A

forms link between F-actin intracellular and the dystroglycan complex in the cell membrane

81
Q

What test can be carried out at birth in DMD?

A

serum creatine kinase
leaks out of damaged muscle cells
massively increased level of DMD from birth before any symptoms occur

82
Q

What sort of mutation is DMD?

A

out of frame mutation

83
Q

What sort of mutation is BMD?

A

in frame mutation

84
Q

What does BMD stand for?

A

Becker muscular dystrophy

85
Q

Describe fragile X syndrome

A

X linked recessive
genetic anticipation
most common inherited cause of learning disability
phenotype in males can be severe
some carrier females are affected but more mildly

86
Q

Describe Edward’s syndrome

A 
trisomy 18
small chin
clenched hands with overlapping fingers
malformations of heart, kidneys etc
if survive first year generally have profound LD
87
Q

Describe patau syndrome

A

trisomy 13
congenital heart disease is usual
about 50% die in first month

88
Q

Describe the clinical features of patau syndrome

A 
cleft lip and palate
micropthalmia
abnormal ears
clenched fists
post axial polydactyly
89
Q

How do trisomies mutations occur?

A

normally from maternal non-disjunction in meiosis

90
Q

What does PGD stand for?

A

Pre-implantation genetic diagnosis

91
Q

What are the pros of PGD?

A

permits implantation of unaffected embryos

TOP then unnecessary

92
Q

What are the cons of PGD?

A

possible long wait
not available to all woman
difficulty with multiples visits and procedures
<50% success

93
Q

Describe genetic counselling

A

providing genetics-related advice and information
information re investigation and interpretation
thinking about implications for relatives

94
Q

What are the main principles of a screening programme?

A 
clearly defined disorder
appreciable frequency
advantage to early diagnosis
few false positives 
few false negatives 
benefits outweigh the costs
95
Q

How is sensitivity calculated?

A

true positives/(all affected)

96
Q

How is specificity calculated?

A

True negatives out of all unaffected

97
Q

What is CUB screening?

A

ultrasound and biochemical testing for Downs syndrome

98
Q

Describe chorionic villous sampling

A

10-12 weeks
1/50 miscarriage
quick results

99
Q

Describe amniocentesis

A

16-18 weeks
1/100 miscarriage
result 1-2 weeks

100
Q

how is DNA sequencing carried out?

A 
automated fluorescent dideoxycytidine (Sanger) sequencing
Massively parallel (next gen) sequencing
101
Q

What is allele-specific (ARMS) PCR used for?

A

for specific known point mutations

102
Q

What is MPLA used for?

A

to look for specific duplications and deletions

103
Q

What is Array CGH used for?

A

to detect abnormalities when the location is not known

104
Q

What is quantitive flouresenct PCR used for?

A

Raoid detection of aneuploidies

105
Q

What are the chromosome based analysis methods?

A

karyotyping

FISH

106
Q

Which tests are used to detect sub-microscopic deletions/duplications?

A

FISH
MLPA (position known)
aCGH

107
Q

What techniques are used to detect point mutations?

A

DNA sequencing or ARMS

108
Q

What can be analysed with NGS?

A

single gene
several genes at once
come
genome

109
Q

What are the steps in data analysis in NGS?

A 
DNA
massively parallel sequencing
FASTQ file
Sequence alignment
BAM file
Variant calling
VCF file
Data filtering steps (removing common variants)
110
Q

WHat is meant by pharmacogenetics?

A

the study of the genetically controlled variation in response to medication

111
Q

Describe ivacaftor

A

G551D - the 3rd most common CF mutation
Blocks opening of CFTR chloride channel
Ivacaftor re-opens the channel

112
Q

Describe examples of future therapies in DMD

A

exon skipping: convert DMD to BMD phenotype by altering splicing patterns to correct the reading frame
or using drugs that allow read-through of premature stop codons

113
Q

What are meant by splicing factors and relate it to DMD

A

proteins necessary for normal splicing of other genes - include “muscle blind” proteins
These are mopped up (sequestered) by the abnormal DMPK mRNA to which they bind.

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