10+11 Chromosomal analysis techniques

Question 1

Describe the process of FISH:

Answer 1

Get probe for region of interest. Denature. Hybridise, wash and counterstain for uninteresting regions.

Question 2

When is FISH used? (4)

Answer 2

Copy number imbalances.
Aneuploidy.
Confirming G-banding/micro-array CGH.
Identifying specific Ca abnormalities.

Question 3

What are the three different FISH probe types and how are they used?

Answer 3

Unique sequence: gene duplication/deletion.
Centromeric: Xsome deletion/repeats.
Paint: translocations.

Question 4

Which diseases are controlled by copy number variations changing susceptibility?
CCl3L1
FCGR3B

Answer 4

High CCl3L1: low HIV risk.

Low FCGR3B: high inflammatory autoimmune disorder risk.

Question 5

Which molecular cytogenetic methods are used to assess copy number? (6).

Answer 5

FISH.
MLPA.
Microarray CGH.
Next generation sequencing.
QF-PCR.
qPCR.

Question 6

What is MLPA?
Used for?
Results?

Answer 6

Multiplex Ligation-dependant Probe Assay.
Detecting abnormal copy numbers.
1.35 = duplication. 0.65 = deletion.

Question 7

How does Microarray CGH work?

Answer 7

Genome wide screen, hybridising sample and control DNA to a microarray chip. Assess ratios between the two.

Question 8

Why are analysts needed to check Microarray CGH results?

Answer 8

Check for pathogenicity.

Question 9

Who is Microarray CGH used in?

Answer 9

Learning disability and dysmorphic infants.

Question 10

Pros (3) and cons (3) of Microarray CGH.

Answer 10

Early diagnosis, high resolution, good accuracy.

Only detects dosage changes, low level mosaics undetected. Detects non pathogenic changes.

Question 11

What is next generation sequencing used for?

Answer 11

Calculating a test to control ratio of genetic material.

Question 12

What is QF-PCR?

What is it used for?

Answer 12

Quantitative Fluorescent PCR. Relies on differences in short tandem repeats between each parent.
Prenatal aneuploidy detection.

Question 13

What is qPCR and what is it used for?

Answer 13

Quantitative comparison vs reference genome and normal control.
Confirms small copy number variations when FISH is unsuitable.

Question 14

When are referrals for blood cytogenetic studies made? (6).

Answer 14

Dysmorphic newborns.
Gender assignment.
Developmental problems. 
Heart defect.
Reproductive problems.
Family studies.

Question 15

What percentage of infertile males have a chromosome change?
What are they?

Answer 15

10%.
47,XXY
Or Y deletion.

Question 16

What is a pachytene cross?

Answer 16

A quadrivalent pairing during meiosis. Occurs in translocations.

Question 17

What types of samples are used for prenatal diagnosis and when are they taken?

Answer 17

Amniocentesis: 16w.
Chorionic villus biopsy: 12w.
Non-invasive prenatal testing: 12w.

Question 18

What is non-invasive prenatal testing and what is it used for?

Answer 18

Maternal blood sample.
Extract circulating free foetal DNA.
Aneuploidy 13, 18, 21.

Question 19

What are the indicators for prenatal diagnosis? (4).

Answer 19

High maternal age.
Serum screen risk.
Abnormal ultrasound scan.
Family history.

Question 20

What analysis is done on amniotic fluid and chorionic villus samples?

Answer 20

DNA extraction for QFPCR.

If result normal, culture cells and do G-banded analysis.

Question 21

What are the advantages and disadvantages of Array CGH use in prenatal diagnosis?

Answer 21

Increased resolution and higher detection rate.

Ethical? Small duplications + autism.

Question 22

Which technique is commonly used in cancer tissue analysis?

Answer 22

FISH.

Question 23

What does Microarray CGH detect?

Answer 23

Detects genomic imbalances at high resolution.