Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

GIM > techniques of cytogentic analysis > Flashcards

techniques of cytogentic analysis Flashcards

1
Q

what 3 methods are used to analyse the whole genome

A

G banding
Next generation sequencing
Microarrays

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

what 3 techniques are used for targeted testing

A

Qf- PCR
MLPA
FISH

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

define convention genetics

A

look at full chromosome under microscope- must be in metaphase.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Molecular genetics

A

looks at specific parts of the human genome.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

How is the procedure of G banding carried out

A 
cell culture
Mitotic arrest- metaphase
Hypotonic salt solution
Fixation
Trypsin and Leishman's stain
Banding AT and GC regions
Lighter bands are AT rich and darker bands are GC rich.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

what stain is commonly used in G banding

A

Trypsin or Leishmans stain

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

what is FISH used to analyse a gene or whole chromosome

A

both.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

How is the procedure for FISH carried out

A

DNA is placed on slide along side a DNA probe with a fluorescence marker
denature probe and DNA in samples that they are single stranded.
Hybiridastion can occur and then wash of the probe

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

what are the 3 types of chromosome probes

A

Unique sequence- light up a small region of the genome

Centromere probe- looks at the number of copies of chromosome, as the repeat sequences around the chromosome are unique.

Paints- cover full chromosome and help locate translocations.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

what is FISH used to detect

A 
copy number variation- centromere probe
Aneuploidy
Confirmation/ clarification of G banding
Confirmation of array CGH
Identify speciifc abnormalities in cancer.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

define copy number variation

A

A DNA segment with a variable copy no. compared with a reference genome

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

what 2 conditions can arise due to copy number variation.

A

Autism and cancer.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Is it both high and low copy number variations that predispose you to certain conditions

A

Yes
High copy no. of CCL3L1 = susceptibility to HIV
Low copy no. of FCGR3B = susceptibility to inflammatory autoimmune disorders

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

define MLPA

A

Multiplex Ligation-dependent Probe Amplification

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

what are 4 steps involved in carried out MLPA.

A

1- denature
2- hybridisation
3- ligate
4- Amplify.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

How does PCR detect different sequences in MLPA apart

A

different size

each probe is produced with a different stuffer sequence length.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

what is microarray CGH used for

A

genome wide screen.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

what is MLPA used for

A

alternative to FISH

Show large numbers of copy variations.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

what sample is microarray CGH carried out on

A

3 ml blood EDTA (also 1-2 ml lithium heparin blood for cell culture)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

How is the procedure for microarray CGH work.

A

DNA and control DNA are labelled with a different probe
each competes for the same site on the microarray
If one colour shines brighter than another then there is a duplication or deletion.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

what is the number of changes in a row are classed as significant enough to be classed as a duplication or deletion

A

3 in a row.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

what are the advantages of microarray CGH

A

Early diagnosis
Looks at 8 individuals one microarray chip.
High resolution = increased diagnostic hit rate
Help to find new genomic imbalances.
Greater accuracy of location/size of imbalances
Information on relevant genes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

what are the disadvantages of microarray CGH

A

Dosage changes only – not balanced rearrangements or mutations
Low level mosaics not detected
Non-pathogenic & uncertain pathogenic changes detected
Needs good quality DNA
Future technologies – analyse mutations and dosage changes, eg exomes, whole genomes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

how is the procedure for next generation sequencing carried out.

A

Extract DNA
Fragment DNA
add molecular barcode
All genome of 1 individual has 1 barcode.
genome is split into different windows, look for dosage differences against controls
look at the control ratio- will show whether it is the same there is a gain or a mutation.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

what does microarrays look for

A

dosage problems

deletions and duplications.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

what does next generation sequencing look for

A

dosage differences.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

what is quantitative fluorescent PCR is used look for what

A

aneuplodies.

28
Q

How is the procedure for quantitative fluorescent PCR carried out.

A

PCR amplification of short tandem repeats (chromosome repeated DNA sequences) using fluorescent markers.
Amplifies DNA between the beginning and the end of repeats
Assess relative amounts of the patient in comparison to the control.

29
Q

How is prenatal aneuploidy detection carried out

A

DNA extraction from amniotic fluid or chorionc villi
PCR amplification – primers from chromosomes 13, 18, 21, X and Y
DNA dosage in up to 4-5 markers/chromosome
aneuploidy =>2 markers with abnormal dosage

30
Q

define microsatellite tetranucleotide repeat marker (STR)

A

satellite repeat sequences which can be analysed in maternal and paternal DNA to determine prenatal aneuplodiy.

31
Q

when is qPCR carried out

A

When FISH unsuitable

32
Q

How long does G banding take

A

30 mins - 4 hours/case

33
Q

How long does fish take

A

10 mins -1 hour/case

34
Q

how long does microarry take

A

10 mins -2 hours/case

35
Q

what long does NGS/qPCR take

A

30 mins – 2 hours per case

36
Q

how long does MLPA/QF PCR take

A

10 mins/30 mins/case

37
Q

what is the use of cytogenetics

A

Diagnosis
Family studies
Assessing reproductive risks
Cancer management

38
Q

what material can be sued to sample cytogenetics

A
  • Blood- best type of sample
  • Amniotic fluid
  • Placenta
  • Other foetal tissue- for spontaneous miscarriages.
  • Bone marrow
  • Tumour
39
Q

With what abnormalities are people often reffered for cytogenetic anaylsis.

A 
dysmorphic new born
gender assignment
developmental problems- intellectual, physical and sexual
heart defect
reproductive problems
family studies..
40
Q

what sample is required for G banding

A

2-5 ml unclothed blood.
stimulate T lymphocytes
Culture 2-3 days.

41
Q

what 2 chromosomes are involved in the down syndrome robertsonian trans location

A

Trivalent formation

meiotic paring.

42
Q

what is the name of the complex formed when carrier is 2 chromosomes join in robersonian translocations during meiosis pairing.

A

Trivalent formation at pachytene

43
Q

In what stage of meiosis 1 does the trivalent form a chain

A

anaphase.

44
Q

do circular structures form in metaphase of meiosis one during robersonian translocation

A

no- because unlike normal structures the telomeres don’t join.

45
Q

what are 2 types of chromosome problems commonly causes fertility problems in the populations

A

balanced chromosome change.

chromosome change- (47XXY or Y deletion)

46
Q

what are the 3 forms of prenatal diagnosis

A
  • Amniocentesis (16w)
  • Chorionic villus biopsy (CVS, 12w)
  • NIPT (12w)- non invasive prenatal technique.
47
Q

which prenatal sampling can be done at the ear lies date (12 weeks) amniocentesis or chronic villas biopsy

A

chronic villus biposy

48
Q

how can a NIPT (12w)- non invasive prenatal technique.

be carried out on the mother of the child

A
  • Maternal blood sample

* Extract circulating free fetal DNA

49
Q

How many miscarriges result due to invasive sampling methods

A

1 in 200

50
Q

what causes infertility problems more commonly balanced translocations or chromosome changes (45X)

A

chromosome changes

51
Q

what are non invasive prenatal testing used to confirm

A

aneuplodies.

52
Q

when should you condor prenatal testing

A

High maternal age
serum screen risk- hormones in others blood can be different if there is a trisomy.
abnormal ultrasound scan (USS)-physical abnormalities visible
FH/previous chromosome abnormality

53
Q

How is the procedure for cytogenetics in amniotic fluid carried out.

A
  1. Portion for DNA extraction (QF-PCR)
  2. Separate cells from remaining fluid-if QFCR abnormal.
  3. Culture cells (7-14 days) if QFPCR result abnormal
  4. G-banded analysis.
54
Q

How is the procedure for cytogentic and chronic villus carried out

A
  1. Separate maternal from foetal tissue
  2. QF-PCR
  3. Culture cells (7-14 days) if QFPCR result abnormal
  4. G-banded analysis
55
Q

how is amniocentesis diagnosis confirmed.

A
  1. QF-PCR – allele ratios from 2 markers indicative of trisomy 21
    cell culture for confirmation
56
Q

In a spontaneous abortion 50% of the times is due to

A

chromosome abnormality

Triploidy, 45,X, trisomy

57
Q

Preimplnatation genetic analyse

A

Testing abnormalities in the blastomere.
Shows dosage changes in cells
Used for individuals who don’t want to undergo invasive techniques.

58
Q

why is cytogenetics used in cancer.

A

Disease specific acquired chromosome changes
– Mostly translocations
– Several different acquired abnormal clones
– Diagnosis
– Prognosis
– Treatment (stratified medicine).

59
Q

what material can be used to test cancer

A

tumour or bone marrow.

60
Q

how is the procedure for testing for leukaemia undertaken

A
  1. 1ml unclotted bone marrow
  2. Suspension culture overnight
  3. G-banded analysis/FISH
    Chromosome quality poor
61
Q

most common translocation in leukaemia

A
  • Translocation between 9 and 22- break on abl (9) and bcr (22)
  • Forms bcrabl fusion gene on chromosome 22.
62
Q

how can you test for the Philadelphia chromosome

A

Probe lights up different for 22 and 9 so if next to each other it shows that the translocation has occurred.

63
Q

how is genetic testing carried out in MYCN gene amplification in neuroblastoma.

A

multiple repeats and copies of the gene.Increased repeats of the gene means you need chemo to be started immediately.

64
Q

what methods of testing are used on a fresh tumour

A

Fresh tumour – FISH or G-banding (culture – 1-20 days)

65
Q

what methods of testing are used on a archived tissue (paraffin embedded)

A

FISH or genotyping

GIM (14 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions