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Genetics Flashcards

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1
Q

Multifactorial diseases recur in _ to _% of family members

A

2-7%

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2
Q

What quantifies the relative contribution of genetic susceptibility to the predisposition to disease in a population?

A

Heritability

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3
Q

List 4 human characteristics that show continuous normal distribution/polygenic inheritance?

A

Blood Pressure
Height
Intelligence
Head circumference

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4
Q

What model accounts for dichotomous multifactorial disorders?

A

Threshold model

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5
Q

______ is the sum of all of the factors which influence development of multifactorial disorder (genetic and environmental)

A

Liability

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6
Q

At what point in a normal distribution will a person express a dichotomous multifactorial disease?

A

Threshold of liability

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7
Q

“Relatives who share genes with X person will also have higher than average susceptibility depending on how many susceptibility genes they inherited”

What term describes this and what pattern of inheritance is X person likely to have?

A

Familial Clustering

Multifactorial Inheritance

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8
Q

What do adoption studies do?

A

Separate effects of genes and family environments

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9
Q

What is it called when two twins show a trait?

A

Concordance

This is higher in monozygotic twins than dizygotic twins, but still less than 100%

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10
Q

What kind of study compares the frequency of a variant in affected patients versus that of a carefully matched control group?

A

Association Study

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11
Q

What kind of inheritance does this describe:

“The disorder is familial but no distinctive pattern of inheritance”

A

Multifactorial

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12
Q

What kind of inheritance does this describe:

“The recurrence risk is greatest among close relatives of the index case”

A

Multifactorial

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13
Q

What kind of inheritance does this describe:
“Risk of recurrence is higher if more than one family member
is affected”

A

Multifactorial

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14
Q

What kind of inheritance does this describe:

“Risk of disease is conditioned by severity”

A

Multifactorial

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15
Q

What kind of inheritance does this describe:

“Recurrence risk changes between populations”

A

Multifactorial

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16
Q

What kind of inheritance does this describe:

“recurrence risk is higher if the proband is of the lesser affected sex”

A

Multifactorial

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17
Q

What is the respective risk for unilateral and bilateral cleft lip and palate?

A

2%, 6%

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18
Q

What condition is caused by narrowing of the pylorus between stomach and intestine leading to obstruction and vomiting?

A

Pyloric Stenosis

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19
Q

Pyloric stenosis is more common in one sex. Name the sex and how much more common it is?

A

5-times more common in baby boys.

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20
Q

In Complement Factor H (CDH), a certain polymorphism confers a >5-fold increased risk to developing X disease.
Name the polymorphism and name X disease.

A

Y402H.

Age related Macular Degeneration.

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21
Q

Name 4 examples of multifactorial disorders with congenital malformations.

A

Cleft lip and palate
Neural tube defects
Pyloric Stenosis
Congenital Heart Disease

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22
Q

Name 4 examples of common adult diseases that are multifactorial disorders.

A 
Diabetes
Epilepsy
Hypertension
Schizophrenia
Manic depression
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23
Q

What do anterior neuropore defects give rise to?

A

Anencephaly

Encephalocele

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24
Q

In neural tube defects, what do defects lower down in lumbar region cause?

A

Spina bifida

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25
Q

What is the recurrence risk of neural tube defects if you have one affected child?

A

4%

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26
Q

What is the recurrence risk of neural tube defects if you have two affected children?

A

10%

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27
Q

Name 3 groups that slight excess of neural tube defects are observed in.

A
  1. Females
  2. First Born
  3. Babies conceived in late winter
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28
Q

What is the major environmental factor implicated in neural tube defects?

A

Maternal folic acid levels which acts via pathway of homocysteine metabolism

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29
Q

Supplementation of diet with folic acid (4mg/day) prior to conception has reduced recurrence risk from _% to _% in families that have NTD?

A

from 4% to 1%

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30
Q

What common polymorphism is found in methylenetetrahydrofolate reductase (MTHFR) gene (involved in neural tube defects)?

A

C677T

This allele is present in 30% of Irish population.

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31
Q

What percentage of Alzheimers Disease cases is inherited?

A

<5%

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32
Q

Name two cognitive Alzheimers disease symptoms

A

Memory Loss

Disorientation

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33
Q

Name four behaviour Alzheimers disease symptoms

A

Anxiety
Delusions
Depression
Insomnia

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34
Q

The APO ε4 polymorphism is associated with:

A

Increased cholesterol and susceptibility to heart disease.

Side note: This allele also increases risk for AD in a dose-dependent manner. This is the predisposing allele.

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35
Q

The APO ε2 polymorphism is associated with:

A

Decreased cholesterol

Side note: This is the protective allele.

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36
Q

Young asymptomatic person with APO ε4/ε4 has __% lifetime risk of developing AD:

A

30%

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37
Q

Name 3 types of clinical sequencing

A
  1. Multigene (panel) sequencing
  2. Whole exome sequencing
  3. Whole genome sequencing
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38
Q

Name 3 types of cytogenetic tests

A
  1. Array Comparative Genomic Hybridisation (aCGH)
  2. G-banding (‘Karyotyping’)
  3. Fluorescence in situ Hybridisation (FISH)
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39
Q

What is constitutional cytogenetic analysis used for?

A
  • Inherited and de novo chromosomal abberations
  • Known chromosomal syndromes e.g. Down syndrome
  • Prenatal diagnosis
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40
Q

What is oncology cytogenetic analysis used for?

A
  • Acquired events

- Chromosome aberrations present only in the cancer cell

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41
Q

When would a constitutional cytogenetic analysis be indicated?

A
  • Newborns displaying dysmorphic features
  • Infants and children displaying development delay e.g. mental disability
  • Miscarriages
  • For prenatal analysis where increase risk of chromosome abnormality
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42
Q

What does neoplasm refer to?

A

An abnormal mass of tissue that forms when cells grow and divide more than they should or do not die when they should. Neoplasms may be benign (not cancer) or malignant (cancer).

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43
Q

Use of cytogenetics in neoplastic disorders?

A

Diagnosis and prognosis of cancers

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44
Q

Name 4 sample types suitable for cytogenetic analysis

A
  1. Blood
  2. Chorionic villi
  3. Bone marrow
  4. Solid tumours
  5. Solid tissue e.g. skin
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45
Q

What is the main test for postnatal indications requiring a chromosome analysis?

A

Array CGH

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46
Q

What are the clinical indications for microarray (aCGH)?

A
  • Clinically significant abnormal growth -short stature, excessive growth, microcephaly, macrocephaly
  • Abnormal clinical phenotype or dysmorphism
  • Multiple congenital abnormalities
  • Mental retardation or developmental delay
  • Suspected deletion/ microdeletion/duplication syndrome
  • X-linked recessive disorder in a female.
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47
Q

Microarray is ___ based

A

DNA based

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48
Q

Karyotype/FISH is ____ based

A

Cell based

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49
Q

What are the clinical indications for Karyotype/FISH analysis?

A
  • Trisomy
  • Numerical sex chromosome abnormality
  • Ambiguous genitalia
  • Family history of chromosome abnormality
  • Mosaicism
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50
Q

What is the resolution of G-banding?

A

3-10Mb

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51
Q

What can aCGH not detect?

A
  1. Balanced rearrangements
  2. Low level mosaicism
  3. Polyploidy (triploidy can be detected on a SNP array)
  4. Uniparental disomy (can be detected on a SNP array)
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52
Q

What do meiotic nonallelic homologous recombination events between low-copy repeats (also known as segmental duplications) cause?

A

Microdeletion/duplication syndromes

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53
Q

Name the best known microdeletion syndrome.

A

DiGeorge syndrome (22q11.2)

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54
Q

What is the gold standard diagnostic test for DiGeorge syndrome?

A

Microarray

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55
Q

Why microarray rather than FISH for the detection of microdeletions?

A

In the event of no deletion the rest of the genome can be investigated

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56
Q

Name 3 types of FISH probes

A
  1. Paint
  2. Centromeric
  3. Locus specific (LSI)
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57
Q

What is the minimum resolution for G-band?

A

5Mb

58
Q

What is the minimum resolution for microarray?

A

50kb

59
Q

What is the minimum resolution for FISH?

A

200kb

60
Q

Name an advantage of G-band tests

A

Can detect balanced rearrangements

61
Q

Name an advantage of Array tests

A

Whole genome screen, higher resolution than G-band

62
Q

Name an advantage of FISH tests

A

Can detect balanced rearrangements; higher resolution than G-band

63
Q

Name a limitation of G-band tests

A

Time consuming, low resolution

64
Q

Name a limitation of Array tests

A

Cannot detect balanced rearrangements or low level mosaicism

65
Q

Name a limitation of FISH

A

Targeted analysis (i.e., need to know what you are looking for)

66
Q

Name 4 molecular genetic samples

A
  1. Blood
  2. Amniocytes
  3. Chorionic villi
  4. Circulating tumour DNA
67
Q

What molecular genetic test is used to diagnose breast cancer?

A

Sequence the entire coding region

68
Q

What molecular genetic test is used to diagnose Huntington Disease (which is always caused by CAG repeat expansion)?

A

Size the repeat region by PCR

69
Q

What is target detection used for in molecular genetic diagnosis?

A

Test for specific characterised mutation in a specific exon of the gene of interest…

  • Family mutation (e.g. BrCa)
  • Commonly known mutations (e.g. CF)
  • Inexpensive, rapid analysis
70
Q

What is scanning detection used for in molecular genetic diagnosis?

A

Analysis of the whole gene for a disorder to determine whether there is a mutation present that could be causing the disease.

  • BrCa, CF (if common mutations are absent)
  • More expensive and more time-consuming
71
Q

Name 4 uses of PCR

A
  1. Detection (e.g. detecting deletions)
  2. Quantitation (Real-time PCR)
  3. Sizing (e.g. Triplet repeat expansions)
  4. Genotyping (e.g. known mutations)
72
Q

What does constitutional microarray analysis do?

A

Reveals gains and losses genome-wide

73
Q

Name 5 applications of next-generation DNA sequencing

A
  1. Targeted resequencing
  2. Gene panels for specific disorders
  3. Whole exome sequencing
  4. Whole genome sequencing
  5. Trisomy sequencing
74
Q

What term describes this: ‘The probability that the test will be negative if the patient does not have the disease’

A

Clinical specificity

75
Q

How many protein-coding genes are in the human genome?

A

20,000-25,000 protein-coding genes

76
Q

What is the term for 1) methylated cytosine and 2) its oxidised form?

A

1) 5-methyl cytosine

2) 5-hydroxy methyl cytosine

77
Q

Name 4 mechanisms of epigenetic regulation

A
  1. DNA methylation
  2. RNA methylation
  3. Post-translational modifications of histones
  4. Antisense regulation
78
Q

What proteins cause DNA to be methylated?

A

DNA methyl transferases (DNMT1, DNMT2, DNMT3)

79
Q

What proteins cause DNA to be demethylated?

A

TETs (Ten-Eleven-Translocation)

80
Q

What conversion do TETs mediate in DNA demethylation?

A

5-methyl-C to 5-hydroxymethyl-C

81
Q

Are histone subunits positively charged or negatively charged?

A

The histone subunits are positively charged, thus allowing the compaction of the negatively charged DNA

82
Q

Name 4 kinds of histone modifications

A
  1. Acetylation
  2. Methylation (lysines)
  3. Phosphorylation
  4. Ubiquitylation
83
Q

Name 4 histones

A

H2A, H2B, H3, H4

84
Q

In loosely packed euchromatin, transcription is ________

A

In loosely packed euchromatin, transcription is active

85
Q

In tightly packed heterochromatin, transcription is ________

A

In tightly packed heterochromatin, transcription is inactive

86
Q

Name 2 functions of long noncoding RNA

A
  1. can facilitate transcription factor binding and thus promote gene activation
  2. may act as scaffolding to stabilise secondary or tertiary structures
87
Q

Name 4 systems epigenetics is involved in:

A
  1. Development
  2. Stem cells
  3. Chromosome X inactivation
  4. Genomic imprinting
88
Q

Name 3 imprinting disorders

A
  1. Prader-Willi Syndrome
  2. Angelman Syndrome
  3. Beckwith-Wieldemann Syndrome
89
Q

What does this describe: “The epigenetic marking of a locus on the basis of parental origin, which results in monoallelic gene expression.”

A

Genomic imprinting

90
Q

How many genes in the human genome are imprinted?

A

> 200 genes

91
Q

When/where are imprints set?

A

In the parental germ cells

92
Q

What is the allele specific gene expression in imprinted genes based on?

A

Parent-of-origin

93
Q

Name 2 paternally expressed imprinted genes (growth promoters)

A

IGF2

PEG1

94
Q

Name 2 maternally expressed imprinted genes (growth suppressors)

A

H19

L23

95
Q

What is the chromosomal region affected in Prader-WIlli Syndrome (PWS) and Angelman Syndrome (AS)?

A

15q11-q13

96
Q

What is the chromosomal region affected in Beckwith Weidemann Syndrome [BWS]/Sporadic Cancer?

A

11p15.5

97
Q

What is the incidence of Prader-Willi Syndrome?

A

1 in 15,000 people

98
Q

What is the key feature of Prader-Willi Syndrome?

A

Constant sense of hunger that usually begins at 2 years of age (Hyperphagia)

99
Q

What is the most common genetic cause of obesity?

A

Prader-Willi Syndrome

100
Q

Name the disorder associated with the following facial features:
Narrow face, almond shaped eyes, small appearing mouth, a thin upper lip with downturned corners of the mouth, crossed-eyes

A

Prader-Willi Syndrome

101
Q

Name the disorder associated with the following clinical presentations:
Profound intellectual deficiency, absent speech, microcephaly, ataxic gait, paroxysmal laughter

A

Angelman Syndrome

102
Q

How is Angelman Syndrome managed?

A
  • Speech therapy
  • Anticonvulsant medication
  • Occupational therapy
103
Q

How is Prader-WIlli Syndrome caused?

A

Paternal loss of 15q (imprinting disorder)

104
Q

How is Angelman Syndrome caused?

A

Maternal loss of 15q (imprinting disorder)

105
Q

What is the candidate gene involved in Prader-Willi Syndrome?

A

SNRPN

106
Q

What is the candidate gene involved in Angelman Syndrome?

A

UBE3A

107
Q

Name the disorder associated with the following clinical presentations:
Pre and postnatal overgrowth of up to 160% of normal birthweight, Macroglossia (protruding tongue), Visceromegaly (enlarged organs), Exomphalos (part of the bowel on the outside)

A

Beckwith-Wiedemann Syndrome

108
Q

What is the estimated risk for tumour development in children with Beckwith-Wiedemann syndrome in the first 8 years of life?

A

7.5%

109
Q

_________ refers to the entire spectrum of genes that determine drug behavior and sensitivity

A

Pharmacogenomics refers to the entire spectrum of genes that determine drug behavior and sensitivity

110
Q

___________ is often used to define the more narrow spectrum of inherited differences in drug metabolism and disposition

A

Pharmacogenetics is often used to define the more narrow spectrum of inherited differences in drug metabolism and disposition

111
Q

Name a drug that exhibits inherited variations in drug metabolism, specifically because of acetylation.

A

Hydralazine.
Hydralazine is an antihypertensive that is inactivated by acetylation. Slow acetylator phenotype can get hydralazine-induced lupus.

Other drugs include sulfonamides and dapsone caffeine.

112
Q

What percentage of Caucasians carry the variant allele TMPT*3A?

A

5%

113
Q

Name 3 drugs that thiopurine S-methyltransferase (TPMT) catalyses the methylation of

A
  1. 6-mercaptopurine
  2. Azathiopurine
  3. Thioguanine
114
Q

Name a genetic polymorphism that is included in drug labelling

A

Thiopurine S-methyltransferase (TPMT) genetic polymorphisms

115
Q

What are people with the TMPT*3A polymorphism at risk of?

A

Life-threatening myelosuppression

116
Q

Name 4 types of drugs that CYP2D6 metabolises

A
  1. Anti-depressants (Fluoxetine)
  2. Neuroleptics (Haloperidol)
  3. Opioids (Codeine)
  4. Antihypertensives (Debrisoquine)
117
Q

What are the molecular genetic mechanisms responsible for variation in CYP2D6 activity?

A
  • Non-synonymous SNPs
  • Gene deletion
  • Gene duplication
118
Q

Cytochrome P450 2D6 (CYP2D6) pharmacogenetics determined using the ratio of debrisoquine to its metabolite, ___________

A

Cytochrome P450 2D6 (CYP2D6) pharmacogenetics determined using the ratio of debrisoquine to its metabolite, 4-hydroxydebrisoquine

119
Q

What are CYP2D6 ultrametabolisers at risk of when given standard codeine doses?

A

Respiratory depression

120
Q

Who has the worst outcomes when treated with tamoxifen?

a) Poor metabolisers
b) Intermediate metabolisers
c) Extensive metabolisers

A

Poor metabolisers

121
Q

What enzymes does the anti-platelet drug, clopidogrel, rely on for activation?

A

CYP3A4 and CYP2C19

122
Q

What is the common dose of clopidogrel?

A

75mg/day

123
Q

Mutations in what gene causes rare cases of warfarin resistance:

A

VKORC1

124
Q

What is a haplotype?

A

Combination of SNPs on a single chromosome

125
Q

VKORC1 haplotype is associated with approximately __% to __% of the variance in the warfarin maintenance dose

A

VKORC1 haplotype is associated with approximately 25% to 30% of the variance in the warfarin maintenance dose

126
Q

Which isomer of warfarin is more potent?

A

S-warfarin is 3-5x more potent than R-warfarin

127
Q

What is S-warfarin metabolised by?

A

CYP2C9

128
Q

What are poor metabolisers of warfarin at increased risk of?

A

Haemorrhage

129
Q

Name two disadvantages of genetic counselling for a patient.

A
  • Psychological burden (guilt/anxiety)

- Implications for relatives

130
Q

A 25 year old girl is seeking predictive testing for a BrCa1 mutation that was found in her mother. What is the risk that she would have inherited the same mutation?

A

50% risk

131
Q

What are the risks of inheriting a BrCa1 mutation?

A

High lifetime risk of breast and ovarian cancer

132
Q

List two reasons why someone may see a genetic counsellor while pregnant? (Prenatal referral)

A
  1. History of miscarriage/foetal abnormalities

2. Abnormality picked up on ultrasound scan

133
Q

Name a disease that commonly results in a genetic counselling referral after new born screening.

A

Cystic Fibrosis

134
Q

What is the success rate of preimplantation genetic diagnosis (PDG)?

A

30% success rate

135
Q

Name two types of invasive testing during pregnancy

A
  1. Chorionic villus sampling (CVS), from between 11-13 weeks

2. Amniocentesis, from 15 weeks

136
Q

Name 2 advantages of gene panels (next generation-sequencing panels)

A
  1. Relatively cheap

2. Fewer unexpected findings

137
Q

Name 2 advantages of whole exome sequencing

A
  1. Don’t need hypothesis

2. Trios more accurate

138
Q

Name 2 disadvantages of whole genome sequencing

A
  1. Risk of unexpected findings

2. Time consuming and difficult to analyse

139
Q

Name 2 types of protein-truncating variants (mutations)

A
  1. Nonsense

2. Frameshift

140
Q

Name a targeted therapy for cystic fibrosis

A

Ivacaftor / Lumacaftor

141
Q

Name an emerging genome editing technique

A

CRISPR/Cas9

Genetics, Perinatal & Paediatrics (4 decks)

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