Lab genetics Flashcards
FISH
Identifies specific changes using fluorescent markers that hybridise to chromosomes
Karyotyping
Uses banding patterns to identify chromosomes and structural changes
Array
Uses tag markers across the genome to show whole-genome copy change
QF-PCR
Uses common variance in repeat lengths to determine copy number
Fragment analysis
Amplifying and comparing obtained length to expected length
TaqMan
Uses paired, labelled probes for a single variant to determine zygosity
(2 probes released that can each bind to specific allele and release gas - used to figure out which allele)
ARMS
Uses paired probe mixes to determine presence / absence of specific variants
MLPA
Copy number determination dependant on probe ligation and amplification
Sanger
Uses chain termination to provide sequence for small regions (usually <1kbp)
What are the 2 types of NGS?
Targeted panel
Clinical exome
How is MSI detected?
PCR
What is MSI sensitive to?
Immunotherapy
How does ARMS work?
One primer only extends if variant present
Other primer only extends if variant absent
When is TaqMan used?
small number of effect alleles
e.g. pharmacogenomics, haemochromatosis, OPMD
When is PCR used?
Aneuploidy
How does Sanger work?
Fluorescent nucleotides in base specific colours
NIPT
Differentiates foetal and maternal cfDNA based on length and creates a foetal:maternal ratio
Euchromatin
Gene rich, stains lightly
Heterochromatin
Gene poor, stains darkly
What is the only method of detecting changes to chromosome structure?
Karyotyping
When is FISH used?
Specific chromosome regions
Eg. Myeloma
Lymphoma
Breast & Gastric Cancer
Monogenic diabetes
Presents like type 1 diabetes at older age
Examples of clinically critical samples
neonates
advanced cancer
dead
separate test requests
separate referrals
When is cell culture used?
Haematological malignancy
Chromosomes are only condensed and visible in ____phase.
meta
In general, ________ cultures produce higher quality cells.
longer
Karyotyping uses _ bands.
G
MLPA steps
DNA denaturation and probes hybridization
Ligation reaction
PCR amplification
Electrophoresis
Data analysis
QF PCR identifies alleles by…
size.
Low level peaks in Sanger sequencing
Mosaicism
Errors in Sanger sequencing
Unclean traces or artifacts
How does NGS work?
Different colours for different bases
What is a pseudogene
A severely mutated gene that can end up in another gene and cause disease
How do arrays work?
Template and patient DNA dyed and bound together to compare
- Deletion - loss of homozygosity
What information does interphase FISH provide?
Presence and absence of genes
What information does metaphase FISH provide?
Specific gene regions
Hemizygous variant
X linked recessive variant in a male
Which translocations can NIPT be used on?
Robertsonian translocations, not complete
Which 2 chromosomes can lose their p arms and become linked by the q arms with no consequence?
13 and 15
Most common Robertsonian translocation (75%)
13-14
Chromosomes in haematological malignancies
Stubby
