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Original Genetics Flashcards

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1
Q

List 3 applications of cytogenetics

A
  1. Chromosomal abnormalities
  2. Microdeletions
  3. Cancer diagnostics
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2
Q

Give an example of a metacentric chromosome

A

Chromosome 2

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3
Q

Give an example of a submetacentric chromosome

A

Chromosome 18

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4
Q

Give an example of an acrocentric chromosome

A

Chromosome 21

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5
Q

Name two classes of chromosomal abnormalities

A
  1. Numerical abnormalities, e.g. Down syndrome

2. Structural abnormalities, e.g. Wolf Hirschhorn syndrome 4p-

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6
Q

What chromosome abnormality is seen in Wolf Hirschhorn syndrome?

A

Del 4p16

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7
Q

What disease are the following characteristics associated with:

  • Wide spaced eyes
  • Prominent nose
  • Delayed growth and development
  • Intellectual disability
  • Seizures
A

Wolf Hirschhorn (del 4p16)

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8
Q

What disease are the following characteristics associated with:

  • Distinctive high-pitched cry that sounds like a cat
  • Intellectual disability and delayed development
  • Widely set eyes (hypertelorism), low-set ears, small jaw, rounded face
A

Cri du Chat (del 5p15)

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9
Q

What disease are the following characteristics associated with:

  • Underdeveloped chin, low-set ears, wide-set eyes, narrow groove in upper lip
  • Variable clinically: Heart defects, poor immune system function
  • ADHD
A

Di George Syndrome

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10
Q

What chromosome abnormality is seen in Cri du Chat syndrome?

A

del 5p15

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11
Q

What chromosome abnormality is seen in Di George syndrome?

A

del 22q11.2

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12
Q

What is the most prevalent behaviour disorder seen in children with 22q11.2 deletion syndrome?

A

ADHD

It is seen in 30-50% of children

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13
Q

What is the most common psychiatric disease that adults with 22q11.2 deletion syndrome develop?

A

1 in 4 develop schizophrenia

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14
Q

What chromosome abnormality is seen in Angelman syndrome?

A

del 15q11-q13

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15
Q

What chromosome abnormality is seen in Prader-Willi syndrome?

A

del 15q11-q13

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16
Q

What type of chromosomal abnormality is seen in the Philadelphia chromosome?

A

Reciprocal translocation

46, XY, t(9:22)(q34.1;q11.2)

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17
Q

What two chromosomes are implicated in the Philadelphia chromosome (bcr-abl)?

A

Chromosome 9 & 22

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18
Q

What kind of chromosomes are involved in a Robertsonian translocation?

A

Translocation between two acrocentric chromosomes.

Balanced rearrangement.

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19
Q

What is a carrier of a Robertsonian translocation at risk of when having a baby?

A

Aneuploid offspring

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20
Q

Polyploidy is a change in chromosome number that is an ____ _____ of the haploid chromosome number

A

Polyploidy is a change in chromosome number that is an exact multiple of the haploid chromosome number

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21
Q

What will triploid foetuses show in the womb?

A

Intrauterine growth retardation

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22
Q

What causes aneuploidy?

A

Non-disjunction of homologous chromosomes at meiosis

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23
Q

List 3 autosomal aneuploidy disorders

A
  • Trisomy 21 (Down syndrome)
  • Trisomy 18 (Edward syndrome)
  • Trisomy 13 (Patau syndrome)
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24
Q

What are 2 common features of autosomal trisomies?

A
  • Intellectual disability

- Congenital abnormalities

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25
Q

What disease are the following characteristics associated with:

  • Simian crease
  • Flat facial profile
  • Congenital heart defects
  • Thick neck skin
A

Down syndrome

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26
Q

What is Down syndrome’s most common karyotype?

A

47, XX, +21

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27
Q

If a parent has a child with Down syndrome, what is the recurrence risk for future pregnancies?

A

1%

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28
Q

Aside from aneuploidy, what other chromosomal abnormality accounts for 4% of down syndrome?

A

Robertsonian translocation.

Usually involves chromosome 14 or 21.
45, XY, t(14,21)

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29
Q

If two parents have a child with translocation Down syndrome, what is the recurrence risk in future pregnancies if the father is the carrier of the translocation?

A

2.5%

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30
Q

If two parents have a child with translocation Down syndrome, what is the recurrence risk in future pregnancies if the mother is the carrier of the translocation?

A

10%

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31
Q

What is the karyotype that accounts for 1% of down syndrome cases? (mosaic karyotype)

A

47, XY,+21/46, XY

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32
Q

What adulthood disease does Down syndrome confer a 100% risk of developing?

A

Early onset Alzheimer’s Disease

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33
Q

What gene is implicated in both Down Syndrome and Alzheimer’s Disease?

A

APP

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34
Q

Name two dosage sensitive genes

A

APP and DSCR1

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35
Q

What is the average incidence of Down syndrome?

A

1 in 650-700

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36
Q

The risk of Down Syndrome increases with….

A

The risk of Down Syndrome increases with age of the mother

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37
Q

When is Meiosis I completed?

A

Ovulation

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38
Q

In first trimester screening, what screening tests are done for Down Syndrome?

A
  • Nuchal translucency thickness scan (NT)

- Maternal serum markers

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39
Q

In second trimester screening, what screening tests are done for Down syndrome?

A

Anomaly scan and quad test - inhibin A

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40
Q

In prenatal diagnosis for Down Syndrome, what procedure is done in first trimester?

A

CVS

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41
Q

In prenatal diagnosis for Down Syndrome, what procedure is done in second trimester?

A

Amniocentesis

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42
Q

What is the sample used for analysis in Non invasive prenatal screening?

A

Cell free DNA (cfDNA) which includes foetal DNA.

Blood can be taken at 9 weeks.

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43
Q

What is the incidence of Edward syndrome?

A

1 in 5000

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44
Q

What is the mortality of Edward syndrome in the first 2 years?

A

90% mortality

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45
Q

What disease are the following characteristics associated with:

  • Prominent occiput
  • Overlapping fingers
  • Rocker bottomed feet
A

Edward syndrome (Trisomy 18)

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46
Q

What disease are the following characteristics associated with:

  • Microphthalmia
  • Cleft lip & palate
  • Post axial polydactylyl
A

Patau Syndrome (Trisomy 13)

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47
Q

What % of infants with Patau syndrome survive past 1 year?

A

10%

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48
Q

Why are imbalances of sex chromosomes better tolerated than autosomal imbalances?

A

X chromosome inactivation

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49
Q

When does X chromosome lyonisation occur?

A

2 weeks after fertilisation

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50
Q

What is the dense mass of sex chromosome that arises from X chromosome lyonisation?

A

Barr body

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51
Q

How many Barr bodies does a normal female have?

A

1

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52
Q

How many Barr bodies does a normal male have?

A

None

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53
Q

What is another name for an inactive X chromosome?

A

Barr body

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54
Q

What is the karyotype for Turner syndrome?

A

45, X

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55
Q

What is the incidence of Turner syndrome?

A

1 in 2000

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56
Q

What chromosome disorder are the following characteristics associated with:

  • Wedding neck
  • Coarctation of aorta
  • Infertility
  • Broad chest and widely spaced nipples
A

Turner Syndrome

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57
Q

What are the clinical features of Turner syndrome due to?

A

Haploinsufficiency of certain genes on X chr e.g. SHOX

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58
Q

What treatment helps improve growth and breast development in Turner Syndrome?

A

Hormonal therapy

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59
Q

What is the incidence of Klinefelter syndrome?

A

1 in 1000

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60
Q

What chromosome disorder are the following characteristics associated with in a min:

  • Infertility
  • Tall stature
  • Breast development
  • High pitched voice
  • Reduced body and facial hair
A

Klinefelter Syndrome

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61
Q

Name 4 types of common variants

A
  • Nonsense
  • Missense
  • Frameshift
  • Large deletion
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62
Q

Give an example of a disease that is affected by a missense point mutation

A

Sickle cell anaemia

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63
Q

Give an example of a disease that is affected by a nonsense point mutation

A

Beta thalassaemia

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64
Q

List the 3 stop codons

A

UAA
UAG
UGA

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65
Q

What specific frameshift deletion is a common cause of autosomal recessive congenital deafness?

A

35delG in connexin 26 gene

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66
Q

What is the most common mutation in cystic fibrosis?

A

del F508

Phenylalanine at position 508

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67
Q

What are the consensus nucleotide sequences involved in splicing? (i.e. all introns start and end with these nucleotides)

A

Almost all introns start with GU and end with AG

68
Q

What is the recurrence risk of autosomal dominant disorder?

A

50%

69
Q

What complication is associated with familial hypercholesterolaemia?

A

Myocardial infarction

70
Q

What receptor has an abnormality in familial hypercholesterolaemia?

A

LDL receptor defect causes increase levels of plasma cholesterol

71
Q

What disorder are these clinical features associated with:

  • formation of distinctive cholesterol deposits(xanthomas) in skin and tendons
  • develop premature atherosclerosis leading to coronary heart disease
A

Familial hypercholesterolaemia

72
Q

Name a disorder that arises from haploinsufficiency

A

Familial hypercholesterolaemia

73
Q

What chromosome is the LDL receptor gene located on? (Familial hypercholesterolaemia)

A

Chromosome 19p

74
Q

What do mutations in familial hypercholesterolaemia cause?

A

Mutations reduce number of functioning LDL receptors

75
Q

Heterozygotes for mutant allele in familial hypercholesterolaemia have ____ fold increased plasma cholesterol levels, while homozygotes have _ fold increased levels.

A

Heterozygotes for mutant allele in familial hypercholesterolaemia have 2-3 fold increased plasma cholesterol levels, while homozygotes have 5 fold increased levels.

76
Q

What treatment is used for familial hypercholesterolaemia?

A
  • Statins

- Gene therapy

77
Q

What enzyme do statins inhibit for the treatment of familial hypercholesterolaemia?

A

HMG CoA reductase

78
Q

What gene is mutated in Marfan syndrome, and what chromosome is it on?

A

FBN1 gene on chr 15

encodes fibrillin-1 protein

79
Q

What 3 body systems are defects found in in Marfan syndrome?

A
  • Ocular
  • Skeletal
  • Cardiovascular
80
Q

What term describes when a gene has effects on multiple aspects of physiology or anatomy?

A

Pleiotropy

81
Q

What pattern of inheritance does Marfan syndrome follow?

A

Autosomal dominant

82
Q

What disorder are the following clinical features associated with:

  • Unusually tall stature, long limbs with long spidery fingers (arachnodactyly), scoliosis
  • Dislocation of the lens
  • Mitral valse prolapse
A

Marfan Syndrome

83
Q

What is the main type of mutation found in Marfan syndrome?

A

Most mutations are missense which act in a dominant negative fashion

84
Q

What pattern of inheritance does Achondroplasia follow?

A

Autosomal dominant

85
Q

What disorder are the following clinical features associated with:

  • Common cause of dwarfism
  • Large head with prominent forehead, shortened limbs
  • Severely dwarfed (adults ~ 4ft), normal IQ
  • Respiratory problems can occur in infants and children due to narrowed nasal passage
A

Achondroplasia

86
Q

What gene is mutated in Achondroplasia and what chromosome is it found on?

A

FGFR3 on chromosome 4p.

Majority of mutations are G to A transition.

87
Q

Is the mutation of FGFR3 in Achondroplasia loss or gain of function?

A

Gain of function mutation - has implications for gene therapy

88
Q

Name a disorder that has 100% penetrance

A

Neurofibromatosis type 1

89
Q

What is the recurrence risk with autosomal recessive disorders?

A

25%

90
Q

What pattern of inheritance do disorders affecting metabolic pathways usually have?

A

Autosomal recessive

91
Q

Name 2 genes that may be mutated in Albinism

A
  1. TYR
  2. TYRP1
    (chromosome 11p)
92
Q

What do 10% of babies with cystic fibrosis present with at birth?

A

Meconium ileus

93
Q

List 2 methods used for the diagnosis of cystic fibrosis

A
  • Sweat test with increased Na+

- Newborn screening program

94
Q

What gene is mutated in cystic fibrosis and what chromosome position does it occupy?

A

CFTR (7q31.2)

95
Q

What other receptor does CFTR work in conjunction with? (especially in the sweat gland epithelium)

A

ENaC

96
Q

List 4 TYPES of mutations that may arise in cystic fibrosis

A
  • Missense
  • Nonsense
  • Splicing
  • Frameshift
97
Q

What is the most common 3bp frame deletion in cystic fibrosis?

A

F508del

98
Q

What is the R117H variant affected by?

A

Poly T tract in intron 8

99
Q

Which T variant of R117H promotes exon 9 splicing?

A

5T variant promotes exon 9 splicing

100
Q

List 2 treatments for cystic fibrosis

A
  1. Antibiotics
  2. Kalydeco
  3. Physiotherapy
101
Q

What is the complication of phenylketonuria if undiagnosed and untreated?

A

Develop hyperphenylalaninemia which impairs brain development

102
Q

What gene is mutated in phenylketonuria?

A

PAH gene resulting in failure to convert phe to tyrosine

103
Q

What test is performed at birth to screen for Phenylketonuria?

A

Guthrie test (heel prick test)

104
Q

If a mother has phenylketonuria and takes excess phe during pregnancy, what does that excess phe act as on the foetus?

A

Excess phe acts as teratogen on developing foetus

105
Q

Name two clinical presentations found among offspring of mothers with phenylketonuria who did not maintain diet during pregnancy?

A
  1. Dysmorphic features

2. Microcephaly

106
Q

What is the most common mutation in Hereditary Haemochromatosis?

A

C282Y in exon 4

107
Q

List 2 disorders seen in travelling community

A
  1. Galactosemia

2. Hurler syndrome

108
Q

What term describes a person with the following:
“because X inactivation is random, carrier females have varying proportion of cells expressing mutant allele and hence can occasionally exhibit signs of disorder”

A

Manifesting heterozygote

109
Q

What gender are X-linked disorders more commonly seen in?

A

Males.

X-linked rec diseases are transmitted by phenotypically normal heterozygous females to sons. But NO male to male transmission.

110
Q

Name 2 common X-linked disorders.

A
  1. Duchenne muscular dystrophy

2. Becker muscular dystrophy

111
Q

What enzyme is increased in Duchenne muscular dystrophy?

A

Increased creatine kinase.

112
Q

What gene is mutated in both Duchenne- and Becker Muscular Dystrophy, and what chromosome is it on?

A

Dystrophin gene at Xp21

113
Q

What type of mutation is usually seen in Duchenne muscular dystrophy?

A

Frameshift

114
Q

What molecular genetic tool is used for the initial genetic screening of Duchenne muscular dystrophy?

A

MPLA or multiplex PCR.

Followed up by full sequencing is MPLA negative.

115
Q

Give 3 examples of mitochondrial disorders.

A
  • Leigh syndrome
  • MELAS
  • MERRF
116
Q

What does MELAS stand for? (Mitochondrial disorder)

A

Mitochondrial encephalomyopathy, lactic acidosis, stroke-like episodes

117
Q

When is the onset for MELAS syndrome?

A

Childhood

118
Q

Is mitochondrial inheritance paternal or maternal inheritance?

A

Maternal inheritance

119
Q

Name 4 complications in inheritance patterns1

A
  1. Penetrance
  2. Expressivity
  3. Mosaicism
  4. Anticipation
120
Q

Name mutated genes that commonly show reduced penetrance

A

BrCa1 and BrCa2

121
Q

Name a disease that shows variable expressivity.

A

Neurofibromatosis

122
Q

What is one explanation of why parents who are apparently normal on genetic testing, can have more than one affected offspring with a dominant genetic disorder?

A

Germline mosaicism

123
Q

What term describes the following:
“Tendency for some disorders to begin at an earlier age and with increased severity with successive generations eg Huntington’s Disease & Myotonic Dystrophy”

A

Anticipation

124
Q

What is one possible explanation for genetic anticipation?

A

Unstable mutation - Expansion of repeated DNA sequences

125
Q

In anticipation disorders, there is a correlation between number of repeats and _____ __ ________

A

In anticipation disorders, there is a correlation between number of repeats and severity of disease

126
Q

In anticipation disorders, there is inverse correlation between number of repeats and ___ __ _____

A

In anticipation disorders, there is inverse correlation between number of repeats and age of onset.

127
Q

What is the pattern of inheritance for Huntington disease?

A

Autosomal dominant

128
Q

What disease are the following clinical presentations associated with:
- Movement disorder accompanied by behavioural changes including aggression, anxiety, apathy, depression and cognitive changes affecting memory, awareness and communication

A

Huntington Disease

129
Q

Name one early stage, middle stage, and late stage motor change in Huntington Disease.

A

Early stage - Restlessness

Middle stage - Trouble with balance and walking

Late stage - Inability to walk

130
Q

What is the penetrance of Huntington Disease?

A

100% penetrant but in age-dependent manner

131
Q

What part of the brain is affected in Huntington Disease?

A

Caudate (Severe atrophy of caudate seen in HD)

132
Q

What mutation repeat is seen in Huntington Disease?

A

CAG repeat in exon 1 of HTT gene on chr 4

133
Q

What range of CAG repeats are necessary to show full penetrance of Huntington Disease?

A

40-120

134
Q

What range of CAG repeats indicate someone is at increased risk of developing Huntington Disease?

A

36-39

135
Q

What disease are the following clinical presentations associated with:

  • Progressive weakness
  • Cataracts
  • Cardiomyopathy
  • Testicular atrophy
  • Frontal baldness in males
A

Myotonic dystrophy (DM1)

136
Q

What two factors complicate the inheritance pattern of Myotonic Dystrophy (DM1)?

A

Variable expression & anticipation

137
Q

Name one complication of congenital myotonic dystrophy

A

Neonatal respiratory distress

138
Q

What nucleotide repeat is expanded in Myotonic Dystrophy (DM1)?

A

Mutation is expansion of CTG normally present in 3’UTR of DMPK gene

139
Q

How does Myotonic Dystrophy (DM2) differ from DM1?

A

DM2 does not show congenital form

140
Q

What nucleotide repeat is expanded in DM2 Myotonic Dystrophy?

A

CCTG expansion in ZNF9 gene

141
Q

How does CTG expansion cause disease?

A

Causes abnormal splicing

142
Q

What is the most common cause of inherited mental retardation?

A

Fragile X syndrome

143
Q

Why is the inheritance pattern of fragile X syndrome considered atypical?

A

Inheritance pattern not fully recessive

144
Q

What is the most single genetic cause of autism spectrum disorders?

A

Fragile X syndrome

145
Q

What nucleotide repeat is expanded in Fragile X syndrome?

A

Mutation is expansion of CGG in the FMR-1 gene

>200 copies in Fragile X syndrome

146
Q

What is the repeat expansion in Fragile X associated with (molecularly)?

A

Repeat expansion is associated with Hypermethylation of DNA and gene silencing. Lack of FMR protein is responsible for signs of Fragile X.

147
Q

What 2 clinical phenotypes are associated with premutation carriers of Fragile X syndrome?

A
  1. Premature ovarian failure

2. FXTAS syndrome

148
Q

What can PCR be used for?

A
  • To detect the presence or absence of a sequence

- To measure the size of a sequence

149
Q

What molecular process does PCR imitate?

A

DNA replication

150
Q

Name 4 components of PCR

A
  1. DNA
  2. Primer
  3. Nucleotides
  4. Taq polymerase
151
Q

Name the 3 key steps in PCR and their temperatures

A
  1. Denaturing DNA (95 C)
  2. Annealing primers (55-60 C)
  3. Extending DNA (72 C)
152
Q

What machine does PCR take place in?

A

Thermocycler

153
Q

List 4 applications of PCR

A
  1. Genotyping
  2. Drug discovery
  3. Mutation screening
  4. Pre-natal diagnosis
154
Q

Name 2 applications of multiplex PCR (amplification of multiple targets in a single PCR experiment)

A
  1. Pathogen detection

2. Exon deletion

155
Q

What molecular genetic tool is used to diagnose deletion-type DMD?

A

Multiplex PCR

156
Q

Name 2 limitations of end-point PCR (i.e. normal PCR)

A
  1. Low sensitivity

2. Not very quantitative

157
Q

What type of PCR allows for the quantitative analysis of gene expression?

A

Real-time PCR (qPCR)

158
Q

What distinguishes the qPCR components from standard end-point PCR (i.e. normal PCR)?

A

The addition of a fluorescent label

159
Q

What molecular genetic tool is described in the following statement:
“A method based on in vitro synthesis of DNA incorporating special chain terminating nucleotides - dideoxynucleoside triphosphates”

A

Dideoxy method of sequencing

160
Q

What general term describes modern sequencing technologies?

A

Next Generation Sequencing (NGS)

161
Q

Is Next Generation Sequencing targeted or not targeted?

A

Not targeted - they sequence everything in the sample

162
Q

List 2 barriers for clinical implementation of NGS

A
  1. Evidence for clinical utility

2. Data interpretation

163
Q

What is the pathogenic mechanism behind Fragile X syndrome?

A

Loss of function due to blocked transcription

164
Q

What is the pathogenic mechanism behind Fragile X associated tremor and ataxia (FXTAS)?

A

Gain of function by pathogenic RNA

165
Q

What is the pathogenic mechanism behind Huntington Disease?

A

Gain of function of a protein

Genetics, Perinatal & Paediatrics (4 decks)

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