10+11 Chromosomal analysis techniques Flashcards
Describe the process of FISH:
Get probe for region of interest. Denature. Hybridise, wash and counterstain for uninteresting regions.
When is FISH used? (4)
Copy number imbalances.
Aneuploidy.
Confirming G-banding/micro-array CGH.
Identifying specific Ca abnormalities.
What are the three different FISH probe types and how are they used?
Unique sequence: gene duplication/deletion.
Centromeric: Xsome deletion/repeats.
Paint: translocations.
Which diseases are controlled by copy number variations changing susceptibility?
CCl3L1
FCGR3B
High CCl3L1: low HIV risk.
Low FCGR3B: high inflammatory autoimmune disorder risk.
Which molecular cytogenetic methods are used to assess copy number? (6).
FISH. MLPA. Microarray CGH. Next generation sequencing. QF-PCR. qPCR.
What is MLPA?
Used for?
Results?
Multiplex Ligation-dependant Probe Assay.
Detecting abnormal copy numbers.
1.35 = duplication. 0.65 = deletion.
How does Microarray CGH work?
Genome wide screen, hybridising sample and control DNA to a microarray chip. Assess ratios between the two.
Why are analysts needed to check Microarray CGH results?
Check for pathogenicity.
Who is Microarray CGH used in?
Learning disability and dysmorphic infants.
Pros (3) and cons (3) of Microarray CGH.
Early diagnosis, high resolution, good accuracy.
Only detects dosage changes, low level mosaics undetected. Detects non pathogenic changes.
What is next generation sequencing used for?
Calculating a test to control ratio of genetic material.
What is QF-PCR?
What is it used for?
Quantitative Fluorescent PCR. Relies on differences in short tandem repeats between each parent.
Prenatal aneuploidy detection.
What is qPCR and what is it used for?
Quantitative comparison vs reference genome and normal control.
Confirms small copy number variations when FISH is unsuitable.
When are referrals for blood cytogenetic studies made? (6).
Dysmorphic newborns. Gender assignment. Developmental problems. Heart defect. Reproductive problems. Family studies.
What percentage of infertile males have a chromosome change?
What are they?
10%.
47,XXY
Or Y deletion.
What is a pachytene cross?
A quadrivalent pairing during meiosis. Occurs in translocations.
What types of samples are used for prenatal diagnosis and when are they taken?
Amniocentesis: 16w.
Chorionic villus biopsy: 12w.
Non-invasive prenatal testing: 12w.
What is non-invasive prenatal testing and what is it used for?
Maternal blood sample.
Extract circulating free foetal DNA.
Aneuploidy 13, 18, 21.
What are the indicators for prenatal diagnosis? (4).
High maternal age.
Serum screen risk.
Abnormal ultrasound scan.
Family history.
What analysis is done on amniotic fluid and chorionic villus samples?
DNA extraction for QFPCR.
If result normal, culture cells and do G-banded analysis.
What are the advantages and disadvantages of Array CGH use in prenatal diagnosis?
Increased resolution and higher detection rate.
Ethical? Small duplications + autism.
Which technique is commonly used in cancer tissue analysis?
FISH.
What does Microarray CGH detect?
Detects genomic imbalances at high resolution.
