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genetics Flashcards

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1
Q

how many pairs of chromosomes does a human have?

structure

A

23

short arm (p) & long arm (q)
joined at centromere

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2
Q

what is a chromosome called when:
i) arms are same length
ii) one arm is longer than other
iii) centromere is situated at top of chromosome

A

i) metacentric
ii) submetacentric
iii) acrocentric

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3
Q

name given to:
i) 1st 22 pairs of chromosomes
ii) 23 pair of chromosomes

A

i) autosomes
ii) sex chromosomes

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4
Q

what is a gene?

How many genes are there in human genome?

A

a specific sequence of DNA that carries the instructions for the construction of a protein

approx 20,000

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5
Q

what is meiosis?

what are the 2 division cycles in meiosis called?

A

division of germ cells to produce ova or sperm

meiosis I
meiosis II

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6
Q

what happens during meiosis I?

A
  1. chromosomes duplicate
  2. recombination = homologous chromosomes align and reciprocal exchange of genetic material occurs between homologous but nonidentical chromatids
  3. diploid number of chromosomes is reduced to half number
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7
Q

what happens during meiosis II?

A

splitting of sister chromatids

(like mitosis but no additional replication)

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8
Q

in female meiosis how many of the 4 daughter cells survive?

A

only 1
(all 4 survive in male meiosisis)

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9
Q

what is aneuploidy?

A

abnormality in number of chromosomes i.e. chromosomes are not haploid

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10
Q

what happens in non-disjunction?

what increases risk of non-discjunction?

A

pairs of homologous chromosomes at **meiosis I **or sister chromatids during mitosis anaphase do not separate so both chromosomes are passed onto 1 daughter cell

therefore:
- 1 daughter cell has 3 chromosomes (trisomy)
- 1 daughter cell is missing 1 chromosome (monosomy)

advanced maternal age

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11
Q

examples of non-disjunction:

A

Down Sydrome (trisomy 21)

Edward’s syndrome (trisomy 18)

Patau syndrome (trisomy 13)

^^ order above = most to least common trisomies

Klinefelter Syndrome (47, XXY)

Turner syndrome (45,X) - most common monosomy identified at birth

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12
Q

Down syndrome
i. mutation

ii.clinical features

A

nondisjunction in 95% (other causes include Robertsonian translocation)

characteristic facial features -upslanting palpebral fissures, epicanthic folds, flat midface, brachycephaly (short anterior-posterior diameter of cranium)

moderate- severe learning difficulties (100%)

cardiac problems (40-50%, VSD, ASD, AVSD)

dementia (10-15%)

ALL

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13
Q

Edward’s syndrome

i. which chromosome is affected
ii. what’s the issue
iii. clinical features

A

poor prenatal/ postnatal outcomes
i. trisomy 18

ii.
meiotic dysjunction
unbalanced Robertsonian translocations (less common)

iii.
survival - usually <1 year

Profound learning difficulties (100%)
Congenital heart disease (90%, commonly VSD)
Facial clefts
Spina bifida
Clenched hands
Rocker-bottom feet

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14
Q

Patau syndrome

i. chromosome affected
ii. genetic cause
iii. clinical features

A

i. trisomy 13

ii. 90% nondysjunction of chromosome 13 (majority of these during maternal meiosis - rest = due to unbalanced translocations (primarily Robertsonian translocations)

iii.
highest rate of spontaneous pregnancy loss of all the trisomies

Profound learning difficulties (100%)
Holoprosencephaly (60–70%) = when brain doesn’t separate into 2 hemispheres properly
Scalp defects
Cleft lip/palate (60–70%)
Microphthalmia/anophthalmia (60–70%)

Congenital heart disease (80%, VSD, ASD)

Postaxial polydactyly (60–70%)

Omphalocele
Renal anomalies

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15
Q

Klinefelter syndrome
i. affected genes
ii. clinical features

A

i. additional sex chromosome 47 XXY

ii. Slightly decreased IQ but within the normal range
Tall stature
feminine fat distribution
small testes
Infertility
Transient gynaecomastia

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16
Q

Klinefelter dx:

A

not usually dx unless incidental finding during:
prenatally
during chorionic villus sampling (CVS) or amniocentesis or in adulthood during infertility investigations

does not cause increase nuchal translucency so not ID on scan

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17
Q

i. hormonal changes in Klinefelter’s:

ii. incidence of Klinefelters

A

hormonal imbalances

FSH, LH ^^
estradiol ^^
SHBG^^ (sex hormone binding globulin)

testosterone vv

ii. 1 in 650 males

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18
Q

triple X syndrome clinical features:

A

Slightly decreased IQ but within the normal range
Tall stature
Normal fertility

usual only found incidentally

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19
Q

XYY syndrome clincial features:

A

Slightly decreased IQ (within the normal range)
Tall stature after puberty
Behavioural problems

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20
Q

Turner syndrome

i. common antenatal feature which prevents survival to term

ii. which finding on USS would make you consider this as dx

iii. clinical features

A

45,X

i. usually do not survive to term due to hydrops fetalis

ii. nuchal translucency >4mm

iii. primary amenorrhoea, delayed puberty

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21
Q

Turner syndrome

i. clinical features

ii. rx:
- to promote puberty
- to prevent osteoporosis

A

i. amenorrhoea (may have spontaneous menstruation due to mosaicism)
delayed puberty
short stature
webbing of neck
cubitus valgus (angling out of forearm at elbow)
widely spaced nipples
cardiac abnormalities (most commonly bicuspid aortic valve)
renal abnormalities

most common cause of gonadal dysgenesis

ii. - low dose ostrogen to promote puberty
- LT hormone replacement to prevent osteoporosis

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22
Q

what are reciprocal translocations?

A

Chromosome rearrangements involving the transfer of genetic material between two nonhomologous chromosomes

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23
Q

most common translocation in humans

A

t(11; 22)(q 23; q 11)

involves chromosome 11 and 22

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24
Q

what happens in Robertsonian translocation?

A

chromosome rearrangement that involves fusion of the long arms of two acrocentric chromosomes and loss of their short arms.

The genes contained on the short arms are represented elsewhere and so their loss does not result in any phenotypic effect of acrocentric chromosomes.

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25
which 5 chromosomes can Robertsonian translocation affect?
only the acrocentric ones!! 13, 14, 15, 21, 22
26
most common Robertsonian translocations (2)
rob (13q; 14q) involves fusion of chromosome 13 to chromosome 14 rob(14q; 21q) involves fusion of chromosome 14 to chromosome 21
27
what is impriting? (in context of Robertsonian translocation) which 2 chromosomes are imprinted genes found on?
process by which one parental allele is preferentially silenced according to its parental origin. 14 & 15
28
what is UPD? which chromosomes can it affect?
uni-parental disomy .... p 277 again only in with chromosome 14 & 15
29
outcome & clinical features of i. maternal UPD 14 ii. paternal UPD 14
i. survive to term --> small, learning difficulties, hypotonia, relative marocephaly ii. spontaneous miscarriage --> (if survive to term) profound LD, feeding diffiuclties, joint contractures
30
outcome of: i. paternal UPD15 ii. maternal UPD 15
i. Angelman syndrome ii. Prader-Willi syndrome
31
Angelman syndrome i. cause ii. clinical features
i. paternal UPD 15 ii. severe learning difficulties characteristic facial appearance ataxic gait
32
Prader-Willi syndrome i. cause ii. clinical features
i. maternal UPD 15 ii. severe learning difficulties poor feeders in neonatal period, then insatiable appetite and overweight hypotonic short stature
33
what are chromosomal microdeletions? how are these usually picked up?
chromosomal deletions that are too small to be detected by light microscopy using conventional cytogenetic methods microarray aCGH
34
common microdeletion syndromes:
5p15 (cri du chat) 7q11 (Williams) 22q11 (DiGeorge)
35
Cri du chat i. mutation ii. clinical features
5p15 deletion Severe learning difficulties Characteristic cat-like cry Characteristic facial appearance with bitemporal narrowing, hypertelorism (wide distance between eyes) and downslanted palpebral fissures
36
Williams syndrome i. mutation ii. clinical features
7q11 Mild to severe learning difficulties Cardiac problems, particularly supravalvular aortic/pulmonary stenosis Renal artery stenosis Characteristic facial appearance with short upturned nose, long philtrum, wide mouth, periorbital fullness ‘Cocktail party personality’ (chatty, interactive behaviour)
37
DiGeorge syndrome i. mutation ii. other names iii. clinical features
22q11 deletion velocardiofacial Shprintzen C- cardiac anomalies (most commonly **tetralogy of Fallot, VSD, interrupted aortic arch**) A - abnormal facies (tubular nose, narrow palpebral fissures and simple ears) T - t-immune cell disorder C- cleft palate H - hypocalcaemia 22 - variable deletion on chromosome 22 Mild to moderate learning difficulties + Short stature Psychiatric disorders Renal anomalies
38
what are missense mutations?
single-base substitutions that have occurred in a coding, critical region of the gene.
39
what is a frameshift mutation?
one or more bases (but not a multiple of three) are inserted or deleted from the usual genetic sequence so disrupting the normal reading frame eventually a new stop codon will be generated resulting in abnormal protein being prematurely truncated
40
what are nonsense mutations?
a single-base substitution that generates a premature stop codon resulting in a truncated protein
41
what do both nonsense and frameshift mutations produce? what are they thus both collectively called?
truncated proteins truncating mutations
42
what is splicing? what are splice mutations?
removal of introns from primary transcript mutations that affect nucleotides at the splice site (junction between introns and extrons)
43
what are exon deletions?
occur when 1 or more exons are deleted in a process that does not constitute an alternative splicing event
44
what causes triplet repeat expansions? examples of triplet repeat conditions? (3) important feature in these conditions? (3)
extensive duplication of a single codon. If this goes beyond a certain threshold you get an abnormal phenotype fragile X syndrome Huntingdon's mytonic dystrophies 1. variability in phenotype 2. anticipation (progression in triplet repeat size and phenotype severity as repeat is passed onto next generation) 3. parent of origin effect (repeat may expand more if passed on by mother than father)
45
4 patterns of inheritance for genes on single locus:
autosomal dominant autosomal recessive X-linked dominant X-linked recessive
46
common autosomal dominant conditions & their genes:
tuberous sclerosis (TSC 1/TSC2) Marfans (fibrillin 1) neurofibromatosis type 1 (NF 1) breast/ ovarian cancer susceptibility (BRCA1/BRCA2) HNPCC (MLH) Huntington's disease (Huntingdin) autosomal dominant polycycstic kidney disease (PKD1/PKD2) achondroplasia (FGFR3)
47
tuberous sclerosis i. affected gene ii. inheritance iii. clinical features iv. which chromosome is mutation on
i. TSC1/TSC2 ii. AD iii.Multisystem disorder characterised by: - cutaneous (angiofibromata, hypomelanotic macules, shagreen patches) - neurological (brain hamartomas causing seizures) - renal (angiomyolipomata) should be strongly suspected **prenatally** if **cardiac rhabdomyosarcomas** are identified iv. chromosome 9 or 16
48
Marfan syndrome i. affected gene ii. inheritance iii. clinical features
i. fibrillin I ii. AD (25% of cases are de novo i.e. not inheritted, v occassionally gene is also recessive?!) iii.Tall stature, arm span to height ratio >1.05, long fingers, dolicocephaly, aortic dilatation and other cardiac anomalies
49
neurofibromatosis type I i. affected gene ii. inheritance iii. clinical features
i. NF1 ii. AD iii. Combination of cafe-au-lait ´ spots, neurofibromata, axillary and inguinal freckling and **optic glioma**
50
breast/ ovarian cancer susceptibility i. affected gene ii. inheritance iii. clinical features
i. BRCA1/ BRCA2 ii. AD iii. BRCA1 60-90% breast ca 40-60% ovarian ca BRCA2 45-80% breast ca 10-30% ovarian ca
51
HNPCC i. affected gene ii. inheritance iii. clinical features
i. MLH ii. AD iii. Inherited predisposition to the development of colon and other cancers including endometrial, gastric and ovarian
52
Huntingdon's disease i. affected gene ii. inheritance iii. clinical features
i. Huntingdin ii. AD iii. Condition characterised by progressive neurological deterioration with dementia, psychiatric disturbance and movement disorder
53
Autosomal dominant polycystic kidney disease i. affected gene ii. inheritance iii. clinical features
i. PKD1/ PKD2 ii. AD iii. Systemic disorder with cysts in the kidneys, liver, pancreas and spleen and cardiovascular anomalies including intracranial aneurysms and **mitral valve prolapse**
54
achondroplasia i. affected gene ii. inheritance iii. clinical features
i. FGFR3 ii. AD iii. Condition characterised by disproportionate short stature with rhizomelic (proximal) shortening and relative macrocephaly
55
if 2 carriers of autosomal recessive gene have children what is the chance of: i child being affected? ii child being carrier
1 in 4 2 in 4
56
common autosomal recessive conditions (& affected gene) :
cystic fibroisis (CFTR) Spinal muscular atrophy (SMN) Tay–Sachs disease (HEXA) Haemochromatosis (HFE) α1-Antitrypsin deficiency (SERPINA1) Congenital adrenal hyperplasia due to 21-hydroxylase deficiency (CYP21A2)
57
cystic fibrosis i. affected gene ii. inheritance iii. features
i. CFTR ii. autosomal recessive iii.chronic pulmonary disease exocrine pancreatic dysfunction male infertility (absence of vas deferens)
58
In Caucasian population: i. what proportion is a CF carrier? ii. what is the chance of a couple having a child with cystic fibrosis?
i. 1 in 20 to 1 in 25 ii. 1 in 400
59
spinal muscular atrophy i. affected gene ii. inheritance iii. features
i. SMN ii. autosomal recessive iii.Characterised by symmetrical proximal muscle weakness; life expectancy ranges from infancy to adulthood depending upon the type of spinal muscular atrophy
60
Tay-Sachs disease i. affected gene ii. inheritance iii. features
i. HEXA ii. autosomal recessive iii. A GM2 gangliosidosis characterised by a ‘cherry-red spot’ on the retina and deteriorating motor and cognitive abilities
61
haemachromatosis i. affected gene ii. inheritance iii. features
i. HFE ii. autosomal recessive iii. Excess absorption of iron with deposition in liver, pancreas and skin leading to cirrhosis, diabetes mellitus and bronzed appearance of skin
62
α1-Antitrypsin deficiency i. affected gene ii. inheritance iii. features
i. SERPINA1 ii. autosomal recessive iii.1 α1-Antitrypsin is a proteinase inhibitor that protects the lungs from elastase; without α1-antitrypsin individuals will develop emphysema at a young age; they may also develop cirrhosis owing to a direct effect of the abnormal α1-antitrypsin on the hepatocytes
63
Congenital adrenal hyperplasia due to 21-hydroxylase deficiency i. affected gene ii. inheritance iii. features
i. CYP21A2 ii. autosomal recessive iii. 2 Attributable to abrogation of 21-hydroxylase, required for the synthesis of cortisol; associated with female virilisation and abnormal puberty (precocious in boys) with or without salt wasting
64
X linked recessive inheritance characteristics
if recessive mutation is on X chromosome males will be affected - only males are affected (if for some reasons females are affected they will have a milder phenotype - there is no male to male transmission - condition may appear to skip conditions
65
examples of X-linked recessive conditions & affected gene:
Duchenne muscular (dystrophin) Haemophilia A (factor VIII gene) ocular albinism (GPR143) X-linked adrenoleucodystrophy (ABCD1) Fragile X Syndrome (FMR 1)
66
Duchenne muscular dystrophy: i. affected gene ii. inheritance iii. features
i. dystrophin ii. X-linked recessive iii. delayed motor development Progressive myopathy affecting proximal muscles causes early loss of ambulation and death in the third decade owing to respiratory failure pseudohypertrophy of calf muscels waddling gait cardiomyopathy (dilated)
67
haemophilia A i. affected gene ii. inheritance iii. features
i. factor VIII gene ii. X-linked recessive iii. Attributable to deficiency of factor VIII, an important component of the clotting cascade; affected male individuals have abnormal clotting, with severe haemophilia A leading to spontaneous joint and muscle bleeding
68
occular albinism i. affected gene ii. inheritance iii. features
i. GPR 143 ii. X-linked recessive iii. Hypopigmentation of iris and retina; associated with poor visual acuity, nystagmus, strabismus and abnormal decussation of the optic nerves
69
X-linked adrenoleucodystrophy i. affected gene ii. inheritance iii. features
i. ABCD 1 ii. X-linked recessive iii. Accumulation of very-long-chain fatty acids in the adrenal glands and brain; results in progressive cognitive deterioration and adrenal failure
70
Fragile X syndrome i. affected gene ii. inheritance iii. features
i. FMR 1 ii. X-linked recessive iii.Caused by expansion of a CGG repeat; results in learning difficulties and characteristic facial appearance
71
X-linked dominant inheritance features:
- manifests v v severely in male fetuses resulting in loss of pregnancy or early neonatal death thus mainly in females
72
X-linked dominant conditions & affected gene
Incontinentia pigmenti (NEMO) Rett syndrome (MECP2)
73
Incontinentia pigmenti i. affected gene ii. inheritance iii. features
i. NEMO ii. x-linked dominant iii. Initially presents as blistering lesions following Blaschko lines; these later become hyperpigmented and eventually appear as atrophic streaks
74
Rett syndrome: i. affected gene ii. inheritance iii. features
i. MECP 2 ii. x-linked recessive iii. Associated with cognitive regression and severe learning difficulties; other characteristic features include hand wringing and stereotypical movements
75
examples of conditions displaying mitochondrial inheritance:
MELAS (mitochondrial encephelomyelopathy with lactic acidosis and stroke-like symptoms) MERRF (myoclonic epilepsy with ragged red fibres) Leigh's disease Subacute necrotising encephelomyelopathy
76
which 2 screening tests are routinely offered and at what gestation?
1. nuchal translucency (11-14 weeks) = sonographic appearance of subcutaneous fluid at back of foetal neck 2. amniocentesis (15-20 weeks)
77
which maternal factor makes NIPT (non-invasive prenatal testing) less accurate?
maternal obesity - lowers % of free foetal DNA
78
associations of thickened nuchal translucency?
Noonan's chromosomal trisomy ???p 283
79
what is the combined test (in foetal abnormality screening)?
uses info from nuchal translucency scan + 2 serum biochemical markers: PAPP-A h β-hCG
80
what is detection rate of trisomy by: i. NT scanning alone ii. combined testing
1. 70-75% (false positive rate 5%) 2. near 90%
81
what are cffDNA tests? what are they used for used for:
circulating free foetal DNA (free foetal DNA is released by apoptotic cells in the placenta - therefore its cells are representative of nuclear content of cells in developing foetus determining sex rhesus D blood typing detection of trisomy 13, 18, 21
82
chorionic villus sampling: i. earliest gestation it's performed at ii. what are the 2 layers of the chorionic villus?
i. 11 weeks ii. aspiration of placental tissue chorionic villus has 2 cell layers: outer = cytotrophoblast (rapidly dividing and invading layer) inner= mesenchymal core
83
how long does it take to get CVS results from i. outer cytotrophoblastic layer ii. inner mesenchymal core which layer is seen as more representative?
i. 1-2 days ii. 1-3 weeks core (as outer layer is established earlier) - therefore if abnormal cytotrophoblastic result must wait for mesenchymal result)
84
what is confined placental mosacisism? what % CVS samples is this seen in?
where chromosomal abnormality is present in placenta but not foetal tissue 1.5%
85
amniocentesis i. gestation performed at ii. which foetal organs are the amiocytes derrived from? iii. how long after procedure are cultured cells from amiocentesis available to harvest?
i. after 15 weeks ii. skin, urinary and GIT iii. 1-3 weeks
86
what are the miscarriage rate after CVS/ amniocentesis? advantage of CVS>amniocentesis?
approx 1% results more rapidly availably
87
i. what is cordocentesis? ii. from what gestation can this be done? iii. associated miscarriage rates?
i. sampling of foetal from umbillical vein ii. 18 weeks iii. 1-2%
88
what is cordocentesis used to asses?
anaemia prenatal infection
89
FISH (fluorescent in situ hybridisation) i. uses ii. advantages iii. disdvantages
i. rapid aneuploidy detection evaluation of unbalanced translocations ii. A good technique for investigating predictable unbalanced chromosome rearrangement iii. spenny labour intensive
90
QF-PCR (quantitatvie fluorescence PCR) i. uses ii. advantages iii. disadvantages
i. rapid aneuploidy detection ii. rapid results cheap iii. Will usually only identify abnormal dosage involving chromosomes 13, 18 or 21
91
MLPA (Multiplex ligation-dependent probe amplification) i. uses ii. advantages iii. disadvantages
i. Rapid aneuploidy detection Evaluation of unbalanced translocations ii. rapid results iii. limited genomic coverage
92
array-CGH (microarray comparatice genomic hybridisation) i. uses ii. advantages iii. disdvantages
i. Rapid aneuploidy detection Detection of microdeletions Detection of microduplications ii. rapid results info re: gene dosage throughout genome iii. New assay, so unclear whether abnormal results are pathogenic variants or polymorphisms
93
lifetime risk of ovarian cancer in general population
1 in 70
94
genes associated with breast ca development (6)
BRCA1 &BRCA2 MMR genes" MSH2, MLH1, MSH6, PMS2
95
BRCA 1 i. lifetime risk of breast Ca ii. lifetime risk of ovarian ca
i. 60-90% breast ca ii. 40-60% ovarian ca
96
BRCA 2 i. lifetime risk of breast ca ii. lifetime risk of ovarian ca
i. 45-80% ii. 10-30% ovarian Ca
97
what's the overall contribution of BRCA 1 and BRCA2 to breast ca (%)?
<2%
98
what is the risk of ovarian ca in women with BRCA 1&2 who opt for prophylactic BSO? what happens to the risk of breast ca?
1% (peritoneal) halved
99
which malignancies are MMR gene alterations most commonly associated with?
colorectal endometrial gastric ovarian
100
risk of endometrial cancer with MMR defects?
50%
101
HNPCC risk of of: i. ovarian cancer? ii. endometrial cancer?
i. 4% ii. 50%
102
how are tumours tested for HNPCC?
immunohistochemistry
103
syndromes associated with ovarian ca (3)
i. HNPCC = the artist formerly known as Lynch syndrome (MMR repair mutation) ii. Peutz- Jegher syndrome iii. Cowden disease
104
Peutz- Jegher syndrome i. what is the mutation? ii. clinical features? iii. what is the lifetime risk of GI malignancy ? iv. what is the lifetime risk of endometrial cancer
i. mutations within the gene encoding serine/threonine protein kinase 11 (LKB1) ii.pigmented macules of the mucous membranes and skin, gastrointestinal polyps iii. 30% iv. 40%
105
aneuploidy risk evaluation what 3 tests are done in 1st trimester?
nuchal translucency nasal bone measurement assessment of blood flow in ductus venosus
106
in trisomy 21 what would you expect to happen to: 1. nuchal translucency 2. nasal bone measurement 3. blood flow in ductus venosus
1. increased 2. absent/ hypoplastic nasal bone 3. absent/ reversed a wave
107
combined testing 1. which trimester is combined test done? 2. what are the 3 parts? 3. what would happen to result in down syndrome?
1. 2nd trimester 2. NT, bHCG, PAPP-A 3. ^^ NT, ^^bHCG, vv PAPP-A
108
1. which semester is triple/ quadruple screen done in? 2. what tests are in the triple screen? 3. what tests are in the quadruple screen? result for these if Down syndrome
1. α-FP + ^^ β-hCG + vv unconjugated oestradiol 2. as above + ^^inhibin

part I (12 decks)

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