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Flashcards in L16 - chromosome abnormalities Deck (105):
1

How many subunits do histones have?

8 - octamer

2

Describe the structure of chromatin

Hanging loops of DNA on a protein scaffold

3

From which type of chromatin are genes expressed?

active chromatin

4

Which types of epigenetic modifications change chromatin from its inactive to active form?

DNA demethylation
Histone acetlyation etc...

5

Which types of epigenetic modifications change chromatin from its active to inactive form?

DNA methylation
Histone deacetylation etc...

6

In epigenetic modification changes are not made to which part of DNA structure?

The DNA sequence is not changed

7

Chromosomes from which part of the cell cycle are used for chromosome analysis?

Metaphase chromosomes

8

How are metaphase chromosomes gathered for chromosome analysis?

Living cell in vitro are cultured, chromosomes are gathered at metaphase by using spindle inhibitors.

9

What is the name of the process whereby chromosomes are systematically sorted?

Karyotyping

10

Different sample types of chromosomes yield chromosomes of different lengths. What different specimen types of chromosomes are used?

Bone marrow
Blood (T-lymphocytes)
Amniotic fluid
CVS (chorionic villus sample)
Solid tissue

11

What does karyotyping involve?

Metaphase chromosomes are:
1. Stained
2. Paired up and grouped together
3. Described using standard nomenclature (ISCN 2013)

12

What type of chromosome contains no eukaryotic genes of consequence on its p arm?

acrocentric chromosomes

13

Which type of chromosome has p and q arms of similar length?

metacentric chromosomes

14

Chromosomes are grouped from A to G by which properties?

Size and shape

15

Which chromosome was incorrectly number and is actually larger than its previous numbered chromosome?

chromosome 22 (is bigger than 21)

16

G-banding is a staining method which uses trypsin to digest proteins which are then stained with Romanowski dye to produce light and dark bands. Why do the dark G (+ve) bands stain darker than the light G (-ve) bands?

Dark G(+ve) bands are AT rich (gene poor)
Light G(-ve) bands are GC rich (gene rich)

17

How many pairs of chromosomes do humans have?

23 pairs

18

How many pairs of autosomes do humans have?

22 pairs

19

How many pairs of sex chromosomes do humans have?

1 pair

20

Describe a normal male karyotype using the correct nomenclature

46,XY, Normal male karyotype

21

What are chromosome ideograms?

Standard diagrams which show the standard banding patterns for each chromosome.
Dark and light bands are numbered according to international convention: ISCN 2014 - therefore international results and research are comparable

22

What is automated karyotyping?

Slides scanned automatically
Images taken
Digital karyotypes from images
Analyse chr's paired up on screen

23

How are chromosomes described in a chromosome report?

Using ISCN 2013 standard format:
1. Chromosome number
2. Sex complement
3. Structural changes
Separated by commas and NO SPACES!

24

Why do cytogenetic analysis?

1. Accurate diagnosis/ prognosis of clinical poblems
2. Better clinical management
3. Assess future reproductive risks
4. Prenatal diagnosis

25

What are the types of constitutional abnormalities (abnormality present from birth) that cause people to be referred for cytogenetic analysis?

1. Prenatal diagnosis
2. Birth defects
3. Abnormal sexual development
4. Infertility
5. Recurrent fetal loss

26

What are the type of acquired abnormalities that cause people to be referred for cytogenetic analysis?

1. Leukaemias
2. Solid tumours
3. Specific translocations/ abnormalities can give prognostic information (advise on best treatment)

27

What is sampled in chorionic villus sampling?

Chorionic villus (placental tissue)

28

What is sample in amniocentesis?

Amniotic fluid containing fetal tissues from the amniotic sac

29

When can CVS be done?

11-12 weeks gestation

30

When can amniocentesis be done?

15 weeks onwards

31

What is the risk of miscarriage with CVS?

1.2% miscarriage risk

32

What is the risk of miscarriage with amniocentesis?

0.8% miscarriage risk

33

What does trisomy 21 cause?

Down syndrome

34

What is meant be aneuploidy?

Loss and gain of whole chromosomes

35

Why does aneuploidy arise?

Due to errors at cell division of meiosis

36

What are the three viable trisomies at birth?

Down Syndrome
Patau syndrome
Edwards syndrome

37

What trisomy causes Edwards syndrome?

Trisomy 18

38

What trisomy causes Patau syndrome?

Trisomy 13

39

Which is the only full monosomy syndrome to be viable?

Turner syndrome 45,X

40

Why is Turner syndrome the only viable monosomy?

X chromosome inactivation

41

What is polyploidy?

The gain of a whole haploid set of chromosomes e.g. 69,XXX

42

What is the most common form of polyploidy?

Polyspermy: fertilisation of an egg by more than one sperm

43

What type of polypoidy is accountable for 2-3% of all pregnancies and approximately 15% of all miscarriages (term deliveries die shortly after birth)?

triploidy
Diploid triploid mosaicism is seen in livebirths

44

What can cause aneuploidy?

1. Non-disjunction at one of the meiotic cell divisions
2. Can occur during cell division -> mosaicism

45

What is meant by mosaicism?

Two cell populations present in an individual

46

What is anaphase lag?

When chromosomes are "left-behind" at cell division. The lagging chromosomes may be lost entirely in mitosis or meiosis

47

What are the causes of anaphase lag?

Defects in spindle function or attachment to chromosomes

48

What is the incidence of Down syndrome?

1 in 650-1000

49

What are individuals with Downs syndrome at higher risk of?

Leukaemia
Early alzheimers

50

What are the signs and symptoms of Down Syndrome?

Hypotonia - decreased muscle tone
Characteristic facial features
Intellectual disability
Heart defects

51

What is the incidence of Edwards syndrome?

1 in 6000

52

What are the signs and symptoms of Edwards syndrome?

Small lower jaw
Prominent occiput (back of head)
Low-set ears
Rocker bottom feet
Overlapping fingers

53

Which sex is Edwards syndrome more common in?

Female predominance

54

What causes Edwards syndrome?

Maternal meiosis II error

55

What is the modal lifespan of a baby with Edwards syndrome?

5-15 days

56

When is Edwards syndrome normally diagnosed?

Prenatally- presents with abnormal scan

57

What are the signs and symptoms of Patau syndrome?

Multiple congenital abnormalities
Polydactyly
Holoprosencephaly (forebrain fails to split into 2 hemispheres) - present from single eye-> cleft lip

58

What is the incidence of Patau syndrome?

1 in 12000

59

What is the lifespan of a baby with Patau syndrome?

Majority die in neonatal period

60

What are the signs and symptoms of Turner syndrome?

Puffy feet
Redundant skin at back of neck (neck webbing)
Short stature
Heart defects
Mild learning difficulties
Infertility

61

Which sex is Turner syndrome most common in?

45,X - therefore only occurs in females

62

What causes phenotypic differences in the presentation of Turner syndrome?

The parental origin of X - majority of cases lack paternal X

63

What is X chromosome inactivation?

Only one X chromosome is ever active in a human cell. This occurs because females have 2 and males have 1, therefore it ensures that they have the same chromosome complement

64

Why is a single X chromosome a problem in Turner syndrome, since X chromosome inactivation occurs to make only a single chromosome active in a human cell anyway?

It affects pairing up of chromosomes at mitosis and meiosis. Although males have a single X chromosome the X and Y chromosomes have short regions in common called the pseudo-autosomal regions which can pair up.

65

Which gene is present in the pseudoautosomal region that is associated with the short stature seen in Turner syndrome?

SHOX gene

66

What is mosaicism?

Presence of 2 or more cell lines in an individual

67

What causes mosaicism?

Usually caused by MITOTIC non-dysjunction

68

Why is the degree of mosaicism in an individual so variable?

Degree of mosaicism depends on when the error occurred:
1. First post zygotic division -> looks like a meiotic event
2. Subsequent divisions -> 3 cell lines (monosomy cell line usually lost - unless X chromosome)

69

What is the meaning of uniparental disomy (UPD)?

Presence of homologous chromosomes from one parent

70

Why does UPD matter?

If the chromosomes is imprinted. Imprinted chromosomes show differential expression of specific genes depending on the parental origin of the chromosome,

71

Why does UPD for the same chromosome cause two different disease: Prader-Willi and Angelman syndrome?

Imprinted genes show differential expression depending on the parental origin of the chromosome.
Prader-Willi syndrome is caused by paternally inherited chromosomes.
Angelman syndrome is caused by maternally inherited chromosomes.

72

List the four "common" mechanisms to generate UPD

1. Trisomy rescue
2. Monosomy rescue
3. Gamete complementation
4. Mitotic error
Each require two separate abnormal events

73

Which is the most common mechanism to generate UPD?

Trisomy rescue

74

What happens in trisomy rescue?

2 abnormal events:
1. Meiotic error -> trisomy
2. Mitotic error-> disomy (1 in 3 chance leads to UPD)

75

How do you test for UPD?

Molecular genetic test using informative repetitive DNA markers on imprinted genes/ regions of interest, to see whether inheritance is bi-parental or not

76

List the cytogenic structural abnormalities you can get

Translocations - Robertsonian and Reciprocal
Inversions - paracentric and pericentric
Deletions - including microdeletions
Duplications
Insertions (into different chromosomes)
Rings
Marker chromosomes - small chromosome with centromere
Isochromosomes

77

What is a reciprocal translocation?

A two-break rearrangement that is usually unique to a family. Carriers produce balanced and unbalanced gametes

78

How do you assess umbalanced segregant outcomes?

1. Establish likely segregation - viable offspring an option?
2. Have the imbalances been reported before?
3. Quote risks if established

79

What is a Robertsonian translocation?

Two acrocentric chromosomes fused together

80

In phenotypically normal, balanced carriers of Robertsonian translocations - how many chromosomes do you see?

45 - only time you see a normal individual with 45 chromosomes

81

How does a Robertsonian translocation pair up during meiosis?

Forms a trivalent - not very stable

82

What are Robertsonian carriers at risk of during meisosis?

Anueploidy

83

Can homologous carriers of Robertsonian translocations have a normal pregnancy?

No - gametes always have a monosomy or trisomy

84

What does der(14;21) mean?

A robertsonian translocation between chromosome 14 and 21.

85

How do deletions arise?

Uneven pairing and recombination during meiosis

86

What is the difference between a terminal and an interstitial deletion?

Terminal deletion - affects ends
Interstitial deletion - within arm

87

What is the effect of deletions on the phenotype?

Likely (but not always) accounts for phenotype

88

What is a microdeletion?

A deletion smaller than 100Kb

89

How can you detect a microdeletion?

Can't always see on G banding as its too small, need to use FISH technique to diagnose and confirm the specific region associated with the phenotype

90

What is FISH?

fluorescent in situ hybridisation

91

What is FISH used for?

To answer SPECIFIC questions. You need to know what you are looking for and therefore which probes to use for specific chromosomes or loci.

92

How is FISH done?

1. Denature chromosome and fluorescently labelled DNA probe to single strand
2. Reanneal - hybridisation
3. Wash to remove unbound probe
4. Visualise using a fluorescent microscope

93

What are locus/ gene specific FISH probes used for?

Microdeletion/ duplication syndromes that are too small to see on G banded chromosomes

94

What are centromere probes used for?

Identifying chromosome of origin, marker chromosomes and copy number analysis

95

What are whole chromosome paints used for?

To identify a chromosome in a rearrangement

96

What are the benefits of using FISH probes for common aneuploidies (13,18,21,X and Y) compared to full karyotypes?

Full karyotypes take up to 14 days as cells need to be cultured, whereas FISH probes can be used on uncultured cells and take 24-48hrs. They also have 99+ % accordance with full karyotype.

97

What different types of probes can be used in Leukaemia FISH and how do they work?

1. Fusion probes - detect translocations of genes involved
2. Breakapart probes - detect gene rearrangement
3. Locus specific probes - detect amplifications e.g. oncogenes, her2, c-myc

98

What are the benefits of microarray methodology?

Examines the whole genome at high resolution

99

What can microarrays detect and not detect?

They can detect copy number changes but can't detect balanced rearrangements or specific mutations which don't results in a copy number change

100

How are microarrays done?

1. Take an equal amount of patient DNA and reference DNA - each with attached green or red fluorescent marker - and mix.
2. Add to array slide spotted with oligonucleotides (60mers)
3. Hybridise for 48 hours
4. Wash slide
5. Scan
6. Input scan images to analysis software - detects ratio of green:red fluorescence and analyses relative copy numbers

101

Who is referred for aCGH?

1. Learning difficulties/developmental delay/multiple congenital abnormalites (15-20% abnormality rate)
2.Normal karyotype
3. Balanced de novo karyotype - is it really balanced?
4. Unbalanced karyotypes to assess gene content

102

What can array platforms detect?

copy number changes
loss of heterozygosity (using SNP)

103

What are the advantages of aCGH?

1. Examines the entire genome at high resolution
2. Targeted against known genetic conditions and sub telomere regions
3. 1 array is equivalent to many thousands of FISH investigations and can be automated
4. Detailed information on genes in del/dup region
5. Better phenotype/ genotype correlation

104

What are the disadvantages of aCGH?

1. Arrays are more expensive than karyotyping
2. Will not detect balanced rearrangements - therefore not suitable for all referrals
3. Copy number variation - genuine abnormality?
4. Mosaicism may be missed

105

What will be future developments for prenatal testing?

1. Microarrays used instead of karyotyping for woman with an abnormal scan
2. Non-invasive prenatal testing (NIPT) - free fetal DNA in maternal plasma tested, enough there to capture from 9 weeks gestation
3. Digital PCR and next generation sequencing technology